├── .Rbuildignore ├── .gitignore ├── DESCRIPTION ├── LICENSE.md ├── NAMESPACE ├── R ├── analysis_counts.R ├── analysis_enrichment_fishers.R ├── analysis_enrichment_gsea.R ├── analysis_enrichment_wilcoxon.R ├── analysis_expressiondiff_limma.R ├── analysis_expressiondiff_test.R ├── analyze_enrichments.R ├── analyze_expressions.R ├── control_asdataframe.R ├── control_enrichment.R ├── control_expression.R ├── control_import.R ├── control_imputation.R ├── control_normalization.R ├── control_stats.R ├── data.R ├── data_annotate.R ├── data_check.R ├── data_codify.R ├── data_experimemntal.R ├── data_export.R ├── data_extract.R ├── data_import.R ├── data_intersection.R ├── data_merge.R ├── data_object.R ├── data_operations.R ├── data_path.R ├── data_reassign.R ├── data_rmmbr.R ├── data_subset.R ├── fasta_digest.R ├── fasta_extract.R ├── fasta_parse.R ├── fasta_peptides.R ├── fasta_regex.R ├── fun_aggregate.R ├── fun_data_io.R ├── fun_data_io_mzTab.R ├── fun_enrichment.R ├── fun_export_config.R ├── fun_hdf.R ├── fun_imputstats.R ├── fun_invlog2.R ├── fun_pairs.R ├── fun_reverselog_transform.R ├── fun_str_normalize.R ├── fun_theme_palette.R ├── fun_transform_center.R ├── fun_transform_log2.R ├── fun_transform_median_subset.R ├── fun_vectors.R ├── fun_venn.R ├── get_accountings.R ├── get_annotations.R ├── get_quant_names.R ├── get_sample_names.R ├── get_unique_variables.R ├── get_variable.R ├── import_munge.R ├── impute_randomforest.R ├── normalization_limma.R ├── normalization_linear.R ├── normalization_loess.R ├── normalization_median.R ├── normalization_randomforest.R ├── normalization_scaled.R ├── normalization_svm.R ├── plot_compexp.R ├── plot_counts.R ├── plot_dynamic_range.R ├── plot_enrichment.R ├── plot_heatmap.R ├── plot_normalization.R ├── plot_pca.R ├── plot_proportion.R ├── plot_quantrank.R ├── plot_save.R ├── plot_variation_cv.R ├── plot_variation_pca.R ├── plot_venn-euler.R ├── plot_volcano.R ├── protein_align.R ├── protein_collapse.R ├── protein_map.R ├── protein_map_munge.R ├── protein_plot.R ├── select_normalization.R ├── stats_contamination.R ├── stats_print.R ├── stats_summary.R ├── table_check.R └── table_export.R ├── README.md ├── _pkgdown.yml ├── data ├── hela_peptides.rda └── hela_proteins.rda ├── docs ├── 404.html ├── LICENSE-text.html ├── LICENSE.html ├── apple-touch-icon-120x120.png ├── apple-touch-icon-152x152.png ├── apple-touch-icon-180x180.png ├── apple-touch-icon-60x60.png ├── apple-touch-icon-76x76.png ├── apple-touch-icon.png ├── articles │ ├── annotating.html │ ├── annotating_files │ │ └── figure-html │ │ │ ├── unnamed-chunk-11-1.png │ │ │ └── unnamed-chunk-12-1.png │ ├── automating.html │ ├── collapsing.html │ ├── collapsing_files │ │ └── figure-html │ │ │ ├── unnamed-chunk-10-1.png │ │ │ ├── unnamed-chunk-13-1.png │ │ │ ├── unnamed-chunk-14-1.png │ │ │ ├── unnamed-chunk-21-1.png │ │ │ ├── unnamed-chunk-22-1.png │ │ │ ├── unnamed-chunk-23-1.png │ │ │ ├── unnamed-chunk-24-1.png │ │ │ ├── unnamed-chunk-30-1.png │ │ │ ├── unnamed-chunk-31-1.png │ │ │ ├── unnamed-chunk-7-1.png │ │ │ └── unnamed-chunk-8-1.png │ ├── data-object.html │ ├── enrichment.html │ ├── enrichment_files │ │ └── figure-html │ │ │ └── unnamed-chunk-5-1.png │ ├── expression.html │ ├── expression_files │ │ └── figure-html │ │ │ ├── unnamed-chunk-4-1.png │ │ │ ├── unnamed-chunk-5-1.png │ │ │ ├── unnamed-chunk-6-1.png │ │ │ ├── unnamed-chunk-7-1.png │ │ │ ├── unnamed-chunk-8-1.png │ │ │ └── unnamed-chunk-9-1.png │ ├── extracting.html │ ├── extracting_files │ │ └── figure-html │ │ │ ├── unnamed-chunk-3-1.png │ │ │ └── unnamed-chunk-5-1.png │ ├── images │ │ ├── proteins_enrichment_knockdown-control.png │ │ ├── uniprot_search_01.png │ │ └── uniprot_search_02.png │ ├── importing.html │ ├── imputing.html │ ├── imputing_files │ │ └── figure-html │ │ │ ├── unnamed-chunk-5-1.png │ │ │ ├── unnamed-chunk-6-1.png │ │ │ ├── unnamed-chunk-8-1.png │ │ │ └── unnamed-chunk-9-1.png │ ├── index.html │ ├── normalizing.html │ ├── normalizing_files │ │ └── figure-html │ │ │ ├── unnamed-chunk-10-1.png │ │ │ ├── unnamed-chunk-11-1.png │ │ │ ├── unnamed-chunk-13-1.png │ │ │ ├── unnamed-chunk-4-1.png │ │ │ ├── unnamed-chunk-5-1.png │ │ │ ├── unnamed-chunk-6-1.png │ │ │ ├── unnamed-chunk-7-1.png │ │ │ ├── unnamed-chunk-8-1.png │ │ │ └── unnamed-chunk-9-1.png │ ├── overview.html │ ├── proteins_enrichment_knockdown-control.png │ ├── subsetting.html │ ├── summarizing.html │ ├── summarizing_files │ │ └── figure-html │ │ │ ├── unnamed-chunk-12-1.png │ │ │ ├── unnamed-chunk-13-1.png │ │ │ ├── unnamed-chunk-14-1.png │ │ │ ├── unnamed-chunk-15-1.png │ │ │ └── unnamed-chunk-16-1.png │ ├── updates.html │ ├── visualizing.html │ ├── visualizing_files │ │ └── figure-html │ │ │ ├── unnamed-chunk-2-1.png │ │ │ ├── unnamed-chunk-3-1.png │ │ │ ├── unnamed-chunk-4-1.png │ │ │ ├── unnamed-chunk-5-1.png │ │ │ ├── unnamed-chunk-7-1.png │ │ │ └── unnamed-chunk-8-1.png │ ├── workflow-importing.html │ ├── workflow-publication.html │ ├── workflow-simple.html │ ├── workflow-userimport.html │ └── workflow-userimport_files │ │ └── figure-html │ │ ├── unnamed-chunk-10-1.png │ │ ├── unnamed-chunk-6-1.png │ │ ├── unnamed-chunk-7-1.png │ │ └── unnamed-chunk-8-1.png ├── authors.html ├── deps │ ├── bootstrap-5.1.3 │ │ ├── bootstrap.bundle.min.js │ │ ├── bootstrap.bundle.min.js.map │ │ └── bootstrap.min.css │ ├── bootstrap-5.2.2 │ │ ├── bootstrap.bundle.min.js │ │ ├── bootstrap.bundle.min.js.map │ │ └── bootstrap.min.css │ ├── bootstrap-5.3.1 │ │ ├── bootstrap.bundle.min.js │ │ ├── bootstrap.bundle.min.js.map │ │ ├── bootstrap.min.css │ │ ├── font.css │ │ └── fonts │ │ │ ├── 1Ptxg8zYS_SKggPN4iEgvnHyvveLxVs9pbCIPrc.woff │ │ │ ├── 1Ptxg8zYS_SKggPN4iEgvnHyvveLxVvaorCIPrc.woff │ │ │ ├── 1adeadb2fe618c5ed46221f15e12b9c8.woff │ │ │ ├── 4iCs6KVjbNBYlgo6ew.woff │ │ │ ├── 4iCs6KVjbNBYlgoKfw7w.woff │ │ │ ├── 4iCv6KVjbNBYlgoCxCvTtA.woff │ │ │ ├── 4iCv6KVjbNBYlgoCxCvjsGyL.woff │ │ │ ├── 6xK1dSBYKcSV-LCoeQqfX1RYOo3qPZ7nsDQ.woff │ │ │ ├── 6xK1dSBYKcSV-LCoeQqfX1RYOo3qPa7j.woff │ │ │ ├── 6xK3dSBYKcSV-LCoeQqfX1RYOo3aPA.woff │ │ │ ├── 6xK3dSBYKcSV-LCoeQqfX1RYOo3qOK7j.woff │ │ │ ├── 6xKydSBYKcSV-LCoeQqfX1RYOo3i54rAkw.woff │ │ │ ├── 6xKydSBYKcSV-LCoeQqfX1RYOo3ig4vAkw.woff │ │ │ ├── 6xKydSBYKcSV-LCoeQqfX1RYOo3ig4vwlxdo.woff │ │ │ ├── 6xKydSBYKcSV-LCoeQqfX1RYOo3ik4zAkw.woff │ │ │ ├── 6xKydSBYKcSV-LCoeQqfX1RYOo3ik4zwlxdo.woff │ │ │ ├── CSR54z1Qlv-GDxkbKVQ_dFsvWNRevw.woff │ │ │ ├── CSR54z1Qlv-GDxkbKVQ_dFsvaNA.woff │ │ │ ├── CSR64z1Qlv-GDxkbKVQ_TOQ.woff │ │ │ ├── CSR64z1Qlv-GDxkbKVQ_fOAKSw.woff │ │ │ ├── HI_diYsKILxRpg3hIP6sJ7fM7PqPMcMnZFqUwX28DBKXhM0.woff │ │ │ ├── HI_diYsKILxRpg3hIP6sJ7fM7PqPMcMnZFqUwX28DMyQhM0.woff │ │ │ ├── HI_jiYsKILxRpg3hIP6sJ7fM7PqlOPHYvDP_W9O7GQTTbI1rSg.woff │ │ │ ├── HI_jiYsKILxRpg3hIP6sJ7fM7PqlOPHYvDP_W9O7GQTTsoprSg.woff │ │ │ ├── JTUHjIg1_i6t8kCHKm4532VJOt5-QNFgpCtZ6Ew9.woff │ │ │ ├── JTUHjIg1_i6t8kCHKm4532VJOt5-QNFgpCtr6Ew9.woff │ │ │ ├── JTUHjIg1_i6t8kCHKm4532VJOt5-QNFgpCuM70w9.woff │ │ │ ├── KFOlCnqEu92Fr1MmEU9fBBc-.woff │ │ │ ├── KFOlCnqEu92Fr1MmEU9vAA.woff │ │ │ ├── KFOlCnqEu92Fr1MmSU5fBBc-.woff │ │ │ ├── KFOlCnqEu92Fr1MmSU5vAA.woff │ │ │ ├── KFOlCnqEu92Fr1MmWUlfBBc-.woff │ │ │ ├── KFOlCnqEu92Fr1MmWUlvAA.woff │ │ │ ├── KFOmCnqEu92Fr1Me5g.woff │ │ │ ├── KFOmCnqEu92Fr1Mu4mxM.woff │ │ │ ├── QGYpz_kZZAGCONcK2A4bGOj8mNhL.woff │ │ │ ├── S6u8w4BMUTPHjxsAXC-s.woff │ │ │ ├── S6u8w4BMUTPHjxswWA.woff │ │ │ ├── S6u9w4BMUTPHh6UVSwiPHw.woff │ │ │ ├── S6u9w4BMUTPHh6UVeww.woff │ │ │ ├── S6u9w4BMUTPHh7USSwiPHw.woff │ │ │ ├── S6u9w4BMUTPHh7USeww.woff │ │ │ ├── S6uyw4BMUTPHjx4wWA.woff │ │ │ ├── S6uyw4BMUTPHvxo.woff │ │ │ ├── UcCO3FwrK3iLTeHuS_fvQtMwCp50KnMw2boKoduKmMEVuFuYMZs.woff │ │ │ ├── UcCO3FwrK3iLTeHuS_fvQtMwCp50KnMw2boKoduKmMEVuI6fMZs.woff │ │ │ ├── UcCO3FwrK3iLTeHuS_fvQtMwCp50KnMw2boKoduKmMEVuLyfMZs.woff │ │ │ ├── XRXI3I6Li01BKofiOc5wtlZ2di8HDFwmRTA.woff │ │ │ ├── XRXI3I6Li01BKofiOc5wtlZ2di8HDGUmRTA.woff │ │ │ ├── XRXI3I6Li01BKofiOc5wtlZ2di8HDLshRTA.woff │ │ │ ├── a98f7a7574819ba83bec6279a2cecd95.woff │ │ │ ├── memQYaGs126MiZpBA-UFUIcVXSCEkx2cmqvXlWq8tWZ0Pw86hd0Rk0ZjaVQ.woff │ │ │ ├── memQYaGs126MiZpBA-UFUIcVXSCEkx2cmqvXlWq8tWZ0Pw86hd0Rk5hkWVAexg.woff │ │ │ ├── memQYaGs126MiZpBA-UFUIcVXSCEkx2cmqvXlWq8tWZ0Pw86hd0Rk5hkaVQ.woff │ │ │ ├── memQYaGs126MiZpBA-UFUIcVXSCEkx2cmqvXlWq8tWZ0Pw86hd0Rk8ZkWVAexg.woff │ │ │ ├── memQYaGs126MiZpBA-UFUIcVXSCEkx2cmqvXlWq8tWZ0Pw86hd0Rk8ZkaVQ.woff │ │ │ ├── memQYaGs126MiZpBA-UFUIcVXSCEkx2cmqvXlWq8tWZ0Pw86hd0Rk_RkaVQ.woff │ │ │ ├── memQYaGs126MiZpBA-UFUIcVXSCEkx2cmqvXlWq8tWZ0Pw86hd0RkxhjaVQ.woff │ │ │ ├── memQYaGs126MiZpBA-UFUIcVXSCEkx2cmqvXlWq8tWZ0Pw86hd0RkyFjWVAexg.woff │ │ │ ├── memQYaGs126MiZpBA-UFUIcVXSCEkx2cmqvXlWq8tWZ0Pw86hd0RkyFjaVQ.woff │ │ │ ├── memSYaGs126MiZpBA-UvWbX2vVnXBbObj2OVZyOOSr4dVJWUgsg-1x4gaVQ.woff │ │ │ ├── memSYaGs126MiZpBA-UvWbX2vVnXBbObj2OVZyOOSr4dVJWUgsg-1y4k.woff │ │ │ ├── memSYaGs126MiZpBA-UvWbX2vVnXBbObj2OVZyOOSr4dVJWUgsgH1y4k.woff │ │ │ ├── memSYaGs126MiZpBA-UvWbX2vVnXBbObj2OVZyOOSr4dVJWUgshZ1y4k.woff │ │ │ ├── memSYaGs126MiZpBA-UvWbX2vVnXBbObj2OVZyOOSr4dVJWUgsiH0B4gaVQ.woff │ │ │ ├── memSYaGs126MiZpBA-UvWbX2vVnXBbObj2OVZyOOSr4dVJWUgsiH0C4k.woff │ │ │ ├── memSYaGs126MiZpBA-UvWbX2vVnXBbObj2OVZyOOSr4dVJWUgsjZ0B4gaVQ.woff │ │ │ ├── memSYaGs126MiZpBA-UvWbX2vVnXBbObj2OVZyOOSr4dVJWUgsjZ0C4k.woff │ │ │ ├── memSYaGs126MiZpBA-UvWbX2vVnXBbObj2OVZyOOSr4dVJWUgsjr0C4k.woff │ │ │ └── q5uGsou0JOdh94bfvQlr.woff │ ├── data-deps.txt │ └── jquery-3.6.0 │ │ ├── jquery-3.6.0.js │ │ ├── jquery-3.6.0.min.js │ │ └── jquery-3.6.0.min.map ├── favicon-16x16.png ├── favicon-32x32.png ├── favicon.ico ├── images │ ├── uniprot_search_01.png │ └── uniprot_search_02.png ├── index.html ├── link.svg ├── logo.png ├── pkgdown.js ├── pkgdown.yml ├── reference │ ├── Rplot001.png │ ├── Rplot002.png │ ├── Rplot003.png │ ├── Rplot004.png │ ├── align_modification.html │ ├── align_peptide.html │ ├── analysis_counts.html │ ├── analyze_enrichments.html │ ├── analyze_expressions.html │ ├── annotate.html │ ├── as.data.frame.tidyproteomics.html │ ├── calc_enrichment.html │ ├── center.html │ ├── check_data.html │ ├── check_pairs.html │ ├── check_table.html │ ├── codify.html │ ├── collapse.html │ ├── compute_compexp.html │ ├── data_import.html │ ├── down_select.html │ ├── enrichment.html │ ├── enrichment_fishersexact.html │ ├── enrichment_gsea.html │ ├── enrichment_wilcoxon.html │ ├── experimental.html │ ├── experimental_groups.html │ ├── export_analysis.html │ ├── export_compexp.html │ ├── export_config.html │ ├── export_quant.html │ ├── expression.html │ ├── expression_limma.html │ ├── expression_test.html │ ├── extract.html │ ├── fasta_digest.html │ ├── fasta_extract.html │ ├── fasta_parse.html │ ├── fasta_peptides.html │ ├── fasta_regex.html │ ├── fgeomean.html │ ├── figures │ │ └── logo.png │ ├── fmean.html │ ├── fmedian.html │ ├── fmin.html │ ├── fsum.html │ ├── get_accountings.html │ ├── get_annotation_terms.html │ ├── get_annotations.html │ ├── get_quant_names.html │ ├── get_sample_names.html │ ├── get_segment.html │ ├── get_unique_variables.html │ ├── get_variables.html │ ├── grapes-like-grapes.html │ ├── hash_vector.html │ ├── hdf.html │ ├── hela_peptides.html │ ├── hela_proteins.html │ ├── import.html │ ├── import_charge.html │ ├── import_extract.html │ ├── import_mbr.html │ ├── import_remove.html │ ├── import_rename.html │ ├── import_split.html │ ├── import_validate.html │ ├── impute.html │ ├── impute.randomforest.html │ ├── impute_byfunction.html │ ├── impute_randomforest.html │ ├── impute_ratio.html │ ├── index.html │ ├── intersect_venn.html │ ├── intersection.html │ ├── invlog2.html │ ├── list_venn.html │ ├── load_local.html │ ├── match_vect.html │ ├── meld.html │ ├── merge.html │ ├── merge.tidyproteomics.html │ ├── merge_quantitative.html │ ├── munge_identifier.html │ ├── normalize.html │ ├── normalize_limma.html │ ├── normalize_linear.html │ ├── normalize_loess.html │ ├── normalize_median.html │ ├── normalize_randomforest.html │ ├── normalize_scaled.html │ ├── normalize_svm.html │ ├── operations.html │ ├── path_to_package_data.html │ ├── plot.tidyproteomics.html │ ├── plot_compexp-1.png │ ├── plot_compexp.html │ ├── plot_counts-1.png │ ├── plot_counts-2.png │ ├── plot_counts.html │ ├── plot_dynamic_range-1.png │ ├── plot_dynamic_range.html │ ├── plot_enrichment-1.png │ ├── plot_enrichment.html │ ├── plot_euler-1.png │ ├── plot_euler-2.png │ ├── plot_euler.html │ ├── plot_heatmap.html │ ├── plot_normalization-1.png │ ├── plot_normalization.html │ ├── plot_pca-1.png │ ├── plot_pca-2.png │ ├── plot_pca-3.png │ ├── plot_pca.html │ ├── plot_proportion-1.png │ ├── plot_proportion-2.png │ ├── plot_proportion.html │ ├── plot_protein-1.png │ ├── plot_protein.html │ ├── plot_quantrank-1.png │ ├── plot_quantrank-2.png │ ├── plot_quantrank-3.png │ ├── plot_quantrank-4.png │ ├── plot_quantrank.html │ ├── plot_save.html │ ├── plot_variation_cv-1.png │ ├── plot_variation_cv.html │ ├── plot_variation_pca-1.png │ ├── plot_variation_pca.html │ ├── plot_venn-1.png │ ├── plot_venn.html │ ├── plot_volcano-1.png │ ├── plot_volcano-2.png │ ├── plot_volcano.html │ ├── print.tidyproteomics.html │ ├── println.html │ ├── protein_map.html │ ├── protein_map_munge.html │ ├── proteins_volcano_knockdown-control.png │ ├── read_data.html │ ├── read_mzTab.html │ ├── reassign.html │ ├── reverselog_transformation.html │ ├── rf_parallel.html │ ├── rm.mbr.html │ ├── save_local.html │ ├── save_table.html │ ├── select_normalization.html │ ├── set_vect.html │ ├── show_annotations.html │ ├── stats_contamination.html │ ├── stats_print.html │ ├── stats_summary.html │ ├── str_normalize.html │ ├── subset.html │ ├── subset.tidyproteomics.html │ ├── summary.tidyproteomics.html │ ├── svm_parallel.html │ ├── table_proteins_expression_knockdown-control.csv │ ├── table_quantrank-1.png │ ├── table_quantrank-2.png │ ├── table_quantrank-3.png │ ├── table_quantrank.html │ ├── theme_palette.html │ ├── tidyproteomics.html │ ├── tidyproteomics_quo.html │ ├── tidyproteomics_quo_name.html │ ├── tidyproteomics_summary.html │ ├── transform_factor.html │ ├── transform_log2.html │ ├── transform_median.html │ └── write_local.html ├── search.json └── sitemap.xml ├── inst └── extdata │ ├── config │ ├── DIA-NN_peptides.tsv │ ├── FragPipe_peptides.tsv │ ├── FragPipe_proteins.tsv │ ├── MaxQuant_peptides.tsv │ ├── MaxQuant_proteins.tsv │ ├── ProteomeDiscoverer_peptides.tsv │ ├── ProteomeDiscoverer_proteins.tsv │ ├── Skyline_peptides.tsv │ ├── mzTab_peptides.tsv │ └── mzTab_proteins.tsv │ └── human.fasta ├── man ├── align_modification.Rd ├── align_peptide.Rd ├── analysis_counts.Rd ├── analyze_enrichments.Rd ├── analyze_expressions.Rd ├── annotate.Rd ├── as.data.frame.tidyproteomics.Rd ├── calc_enrichment.Rd ├── center.Rd ├── check_data.Rd ├── check_pairs.Rd ├── check_table.Rd ├── codify.Rd ├── collapse.Rd ├── compute_compexp.Rd ├── data_import.Rd ├── down_select.Rd ├── enrichment.Rd ├── enrichment_fishersexact.Rd ├── enrichment_gsea.Rd ├── enrichment_wilcoxon.Rd ├── experimental.Rd ├── experimental_groups.Rd ├── export_analysis.Rd ├── export_compexp.Rd ├── export_config.Rd ├── export_quant.Rd ├── expression.Rd ├── expression_limma.Rd ├── expression_test.Rd ├── extract.Rd ├── fasta_digest.Rd ├── fasta_extract.Rd ├── fasta_parse.Rd ├── fasta_peptides.Rd ├── fasta_regex.Rd ├── fgeomean.Rd ├── figures │ └── logo.png ├── fmean.Rd ├── fmedian.Rd ├── fmin.Rd ├── fsum.Rd ├── get_accountings.Rd ├── get_annotation_terms.Rd ├── get_annotations.Rd ├── get_quant_names.Rd ├── get_sample_names.Rd ├── get_segment.Rd ├── get_unique_variables.Rd ├── get_variables.Rd ├── grapes-like-grapes.Rd ├── hash_vector.Rd ├── hdf.Rd ├── hela_peptides.Rd ├── hela_proteins.Rd ├── import.Rd ├── import_extract.Rd ├── import_mbr.Rd ├── import_remove.Rd ├── import_rename.Rd ├── import_split.Rd ├── import_validate.Rd ├── impute.Rd ├── impute.randomforest.Rd ├── impute_ratio.Rd ├── intersect_venn.Rd ├── intersection.Rd ├── invlog2.Rd ├── list_venn.Rd ├── load_local.Rd ├── match_vect.Rd ├── meld.Rd ├── merge.Rd ├── merge_quantitative.Rd ├── munge_identifier.Rd ├── normalize.Rd ├── normalize_limma.Rd ├── normalize_linear.Rd ├── normalize_loess.Rd ├── normalize_median.Rd ├── normalize_randomforest.Rd ├── normalize_scaled.Rd ├── normalize_svm.Rd ├── operations.Rd ├── path_to_package_data.Rd ├── plot.tidyproteomics.Rd ├── plot_compexp.Rd ├── plot_counts.Rd ├── plot_dynamic_range.Rd ├── plot_enrichment.Rd ├── plot_euler.Rd ├── plot_heatmap.Rd ├── plot_normalization.Rd ├── plot_pca.Rd ├── plot_proportion.Rd ├── plot_protein.Rd ├── plot_quantrank.Rd ├── plot_save.Rd ├── plot_variation_cv.Rd ├── plot_variation_pca.Rd ├── plot_venn.Rd ├── plot_volcano.Rd ├── print.tidyproteomics.Rd ├── println.Rd ├── protein_map.Rd ├── protein_map_munge.Rd ├── read_data.Rd ├── read_mzTab.Rd ├── reassign.Rd ├── reverselog_transformation.Rd ├── rf_parallel.Rd ├── rm.mbr.Rd ├── save_local.Rd ├── save_table.Rd ├── select_normalization.Rd ├── set_vect.Rd ├── show_annotations.Rd ├── stats_contamination.Rd ├── stats_print.Rd ├── stats_summary.Rd ├── str_normalize.Rd ├── subset.tidyproteomics.Rd ├── summary.tidyproteomics.Rd ├── svm_parallel.Rd ├── table_quantrank.Rd ├── theme_palette.Rd ├── tidyproteomics.Rd ├── tidyproteomics_quo.Rd ├── tidyproteomics_quo_name.Rd ├── tidyproteomics_summary.Rd ├── transform_factor.Rd ├── transform_log2.Rd ├── transform_median.Rd └── write_local.Rd ├── pkgdown └── favicon │ ├── apple-touch-icon-120x120.png │ ├── apple-touch-icon-152x152.png │ ├── apple-touch-icon-180x180.png │ ├── apple-touch-icon-60x60.png │ ├── apple-touch-icon-76x76.png │ ├── apple-touch-icon.png │ ├── favicon-16x16.png │ ├── favicon-32x32.png │ └── favicon.ico ├── tests ├── test_import.R ├── testthat.R └── testthat │ ├── test-fun_hdf.R │ ├── test-fun_invlog2.R │ └── test-fun_str_normalize.R ├── tidyproteomics.Rproj └── vignettes ├── annotating.Rmd ├── automating.Rmd ├── collapsing.Rmd ├── data-object.Rmd ├── enrichment.Rmd ├── expression.Rmd ├── extracting.Rmd ├── images ├── proteins_enrichment_knockdown-control.png ├── proteins_volcano_knockdown-control.png ├── table_proteins_enrichment_knockdown-control.csv ├── table_proteins_expression_knockdown-control.csv ├── uniprot_search_01.png └── uniprot_search_02.png ├── importing.Rmd ├── imputing.Rmd ├── normalizing.Rmd ├── overview.Rmd ├── subsetting.Rmd ├── summarizing.Rmd ├── updates.Rmd ├── visualizing.Rmd ├── workflow-importing.Rmd ├── workflow-publication.Rmd ├── workflow-simple.Rmd └── workflow-userimport.Rmd /.Rbuildignore: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jeffsocal/tidyproteomics/HEAD/.Rbuildignore -------------------------------------------------------------------------------- /.gitignore: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jeffsocal/tidyproteomics/HEAD/.gitignore -------------------------------------------------------------------------------- /DESCRIPTION: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jeffsocal/tidyproteomics/HEAD/DESCRIPTION -------------------------------------------------------------------------------- /LICENSE.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jeffsocal/tidyproteomics/HEAD/LICENSE.md -------------------------------------------------------------------------------- /NAMESPACE: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jeffsocal/tidyproteomics/HEAD/NAMESPACE -------------------------------------------------------------------------------- /R/analysis_counts.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jeffsocal/tidyproteomics/HEAD/R/analysis_counts.R -------------------------------------------------------------------------------- /R/analysis_enrichment_fishers.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jeffsocal/tidyproteomics/HEAD/R/analysis_enrichment_fishers.R -------------------------------------------------------------------------------- /R/analysis_enrichment_gsea.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jeffsocal/tidyproteomics/HEAD/R/analysis_enrichment_gsea.R -------------------------------------------------------------------------------- /R/analysis_enrichment_wilcoxon.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jeffsocal/tidyproteomics/HEAD/R/analysis_enrichment_wilcoxon.R -------------------------------------------------------------------------------- /R/analysis_expressiondiff_limma.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jeffsocal/tidyproteomics/HEAD/R/analysis_expressiondiff_limma.R -------------------------------------------------------------------------------- /R/analysis_expressiondiff_test.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jeffsocal/tidyproteomics/HEAD/R/analysis_expressiondiff_test.R -------------------------------------------------------------------------------- /R/analyze_enrichments.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jeffsocal/tidyproteomics/HEAD/R/analyze_enrichments.R -------------------------------------------------------------------------------- /R/analyze_expressions.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jeffsocal/tidyproteomics/HEAD/R/analyze_expressions.R -------------------------------------------------------------------------------- /R/control_asdataframe.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jeffsocal/tidyproteomics/HEAD/R/control_asdataframe.R -------------------------------------------------------------------------------- /R/control_enrichment.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jeffsocal/tidyproteomics/HEAD/R/control_enrichment.R -------------------------------------------------------------------------------- /R/control_expression.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jeffsocal/tidyproteomics/HEAD/R/control_expression.R -------------------------------------------------------------------------------- /R/control_import.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jeffsocal/tidyproteomics/HEAD/R/control_import.R -------------------------------------------------------------------------------- /R/control_imputation.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jeffsocal/tidyproteomics/HEAD/R/control_imputation.R -------------------------------------------------------------------------------- /R/control_normalization.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jeffsocal/tidyproteomics/HEAD/R/control_normalization.R -------------------------------------------------------------------------------- /R/control_stats.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jeffsocal/tidyproteomics/HEAD/R/control_stats.R -------------------------------------------------------------------------------- /R/data.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jeffsocal/tidyproteomics/HEAD/R/data.R -------------------------------------------------------------------------------- /R/data_annotate.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jeffsocal/tidyproteomics/HEAD/R/data_annotate.R -------------------------------------------------------------------------------- /R/data_check.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jeffsocal/tidyproteomics/HEAD/R/data_check.R -------------------------------------------------------------------------------- /R/data_codify.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jeffsocal/tidyproteomics/HEAD/R/data_codify.R -------------------------------------------------------------------------------- /R/data_experimemntal.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jeffsocal/tidyproteomics/HEAD/R/data_experimemntal.R -------------------------------------------------------------------------------- /R/data_export.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jeffsocal/tidyproteomics/HEAD/R/data_export.R -------------------------------------------------------------------------------- /R/data_extract.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jeffsocal/tidyproteomics/HEAD/R/data_extract.R -------------------------------------------------------------------------------- /R/data_import.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jeffsocal/tidyproteomics/HEAD/R/data_import.R -------------------------------------------------------------------------------- /R/data_intersection.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jeffsocal/tidyproteomics/HEAD/R/data_intersection.R -------------------------------------------------------------------------------- /R/data_merge.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jeffsocal/tidyproteomics/HEAD/R/data_merge.R -------------------------------------------------------------------------------- /R/data_object.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jeffsocal/tidyproteomics/HEAD/R/data_object.R -------------------------------------------------------------------------------- /R/data_operations.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jeffsocal/tidyproteomics/HEAD/R/data_operations.R -------------------------------------------------------------------------------- /R/data_path.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jeffsocal/tidyproteomics/HEAD/R/data_path.R -------------------------------------------------------------------------------- /R/data_reassign.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jeffsocal/tidyproteomics/HEAD/R/data_reassign.R -------------------------------------------------------------------------------- /R/data_rmmbr.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jeffsocal/tidyproteomics/HEAD/R/data_rmmbr.R -------------------------------------------------------------------------------- /R/data_subset.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jeffsocal/tidyproteomics/HEAD/R/data_subset.R -------------------------------------------------------------------------------- /R/fasta_digest.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jeffsocal/tidyproteomics/HEAD/R/fasta_digest.R -------------------------------------------------------------------------------- /R/fasta_extract.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jeffsocal/tidyproteomics/HEAD/R/fasta_extract.R -------------------------------------------------------------------------------- /R/fasta_parse.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jeffsocal/tidyproteomics/HEAD/R/fasta_parse.R -------------------------------------------------------------------------------- /R/fasta_peptides.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jeffsocal/tidyproteomics/HEAD/R/fasta_peptides.R -------------------------------------------------------------------------------- /R/fasta_regex.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jeffsocal/tidyproteomics/HEAD/R/fasta_regex.R -------------------------------------------------------------------------------- /R/fun_aggregate.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jeffsocal/tidyproteomics/HEAD/R/fun_aggregate.R -------------------------------------------------------------------------------- /R/fun_data_io.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jeffsocal/tidyproteomics/HEAD/R/fun_data_io.R -------------------------------------------------------------------------------- /R/fun_data_io_mzTab.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jeffsocal/tidyproteomics/HEAD/R/fun_data_io_mzTab.R -------------------------------------------------------------------------------- /R/fun_enrichment.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jeffsocal/tidyproteomics/HEAD/R/fun_enrichment.R -------------------------------------------------------------------------------- /R/fun_export_config.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jeffsocal/tidyproteomics/HEAD/R/fun_export_config.R -------------------------------------------------------------------------------- /R/fun_hdf.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jeffsocal/tidyproteomics/HEAD/R/fun_hdf.R -------------------------------------------------------------------------------- /R/fun_imputstats.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jeffsocal/tidyproteomics/HEAD/R/fun_imputstats.R -------------------------------------------------------------------------------- /R/fun_invlog2.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jeffsocal/tidyproteomics/HEAD/R/fun_invlog2.R -------------------------------------------------------------------------------- /R/fun_pairs.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jeffsocal/tidyproteomics/HEAD/R/fun_pairs.R -------------------------------------------------------------------------------- /R/fun_reverselog_transform.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jeffsocal/tidyproteomics/HEAD/R/fun_reverselog_transform.R -------------------------------------------------------------------------------- /R/fun_str_normalize.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jeffsocal/tidyproteomics/HEAD/R/fun_str_normalize.R -------------------------------------------------------------------------------- /R/fun_theme_palette.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jeffsocal/tidyproteomics/HEAD/R/fun_theme_palette.R -------------------------------------------------------------------------------- /R/fun_transform_center.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jeffsocal/tidyproteomics/HEAD/R/fun_transform_center.R -------------------------------------------------------------------------------- /R/fun_transform_log2.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jeffsocal/tidyproteomics/HEAD/R/fun_transform_log2.R -------------------------------------------------------------------------------- /R/fun_transform_median_subset.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jeffsocal/tidyproteomics/HEAD/R/fun_transform_median_subset.R -------------------------------------------------------------------------------- /R/fun_vectors.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jeffsocal/tidyproteomics/HEAD/R/fun_vectors.R -------------------------------------------------------------------------------- /R/fun_venn.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jeffsocal/tidyproteomics/HEAD/R/fun_venn.R -------------------------------------------------------------------------------- /R/get_accountings.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jeffsocal/tidyproteomics/HEAD/R/get_accountings.R -------------------------------------------------------------------------------- /R/get_annotations.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jeffsocal/tidyproteomics/HEAD/R/get_annotations.R -------------------------------------------------------------------------------- /R/get_quant_names.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jeffsocal/tidyproteomics/HEAD/R/get_quant_names.R -------------------------------------------------------------------------------- /R/get_sample_names.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jeffsocal/tidyproteomics/HEAD/R/get_sample_names.R -------------------------------------------------------------------------------- /R/get_unique_variables.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jeffsocal/tidyproteomics/HEAD/R/get_unique_variables.R -------------------------------------------------------------------------------- /R/get_variable.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jeffsocal/tidyproteomics/HEAD/R/get_variable.R -------------------------------------------------------------------------------- /R/import_munge.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jeffsocal/tidyproteomics/HEAD/R/import_munge.R -------------------------------------------------------------------------------- /R/impute_randomforest.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jeffsocal/tidyproteomics/HEAD/R/impute_randomforest.R -------------------------------------------------------------------------------- /R/normalization_limma.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jeffsocal/tidyproteomics/HEAD/R/normalization_limma.R -------------------------------------------------------------------------------- /R/normalization_linear.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jeffsocal/tidyproteomics/HEAD/R/normalization_linear.R -------------------------------------------------------------------------------- /R/normalization_loess.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jeffsocal/tidyproteomics/HEAD/R/normalization_loess.R -------------------------------------------------------------------------------- /R/normalization_median.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jeffsocal/tidyproteomics/HEAD/R/normalization_median.R -------------------------------------------------------------------------------- /R/normalization_randomforest.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jeffsocal/tidyproteomics/HEAD/R/normalization_randomforest.R -------------------------------------------------------------------------------- /R/normalization_scaled.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jeffsocal/tidyproteomics/HEAD/R/normalization_scaled.R -------------------------------------------------------------------------------- /R/normalization_svm.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jeffsocal/tidyproteomics/HEAD/R/normalization_svm.R -------------------------------------------------------------------------------- /R/plot_compexp.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jeffsocal/tidyproteomics/HEAD/R/plot_compexp.R -------------------------------------------------------------------------------- /R/plot_counts.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jeffsocal/tidyproteomics/HEAD/R/plot_counts.R -------------------------------------------------------------------------------- /R/plot_dynamic_range.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jeffsocal/tidyproteomics/HEAD/R/plot_dynamic_range.R -------------------------------------------------------------------------------- /R/plot_enrichment.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jeffsocal/tidyproteomics/HEAD/R/plot_enrichment.R -------------------------------------------------------------------------------- /R/plot_heatmap.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jeffsocal/tidyproteomics/HEAD/R/plot_heatmap.R -------------------------------------------------------------------------------- /R/plot_normalization.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jeffsocal/tidyproteomics/HEAD/R/plot_normalization.R -------------------------------------------------------------------------------- /R/plot_pca.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jeffsocal/tidyproteomics/HEAD/R/plot_pca.R -------------------------------------------------------------------------------- /R/plot_proportion.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jeffsocal/tidyproteomics/HEAD/R/plot_proportion.R -------------------------------------------------------------------------------- /R/plot_quantrank.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jeffsocal/tidyproteomics/HEAD/R/plot_quantrank.R -------------------------------------------------------------------------------- /R/plot_save.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jeffsocal/tidyproteomics/HEAD/R/plot_save.R -------------------------------------------------------------------------------- /R/plot_variation_cv.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jeffsocal/tidyproteomics/HEAD/R/plot_variation_cv.R -------------------------------------------------------------------------------- /R/plot_variation_pca.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jeffsocal/tidyproteomics/HEAD/R/plot_variation_pca.R -------------------------------------------------------------------------------- /R/plot_venn-euler.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jeffsocal/tidyproteomics/HEAD/R/plot_venn-euler.R -------------------------------------------------------------------------------- /R/plot_volcano.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jeffsocal/tidyproteomics/HEAD/R/plot_volcano.R -------------------------------------------------------------------------------- /R/protein_align.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jeffsocal/tidyproteomics/HEAD/R/protein_align.R -------------------------------------------------------------------------------- /R/protein_collapse.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jeffsocal/tidyproteomics/HEAD/R/protein_collapse.R -------------------------------------------------------------------------------- /R/protein_map.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jeffsocal/tidyproteomics/HEAD/R/protein_map.R -------------------------------------------------------------------------------- /R/protein_map_munge.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jeffsocal/tidyproteomics/HEAD/R/protein_map_munge.R -------------------------------------------------------------------------------- /R/protein_plot.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jeffsocal/tidyproteomics/HEAD/R/protein_plot.R -------------------------------------------------------------------------------- /R/select_normalization.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jeffsocal/tidyproteomics/HEAD/R/select_normalization.R -------------------------------------------------------------------------------- /R/stats_contamination.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jeffsocal/tidyproteomics/HEAD/R/stats_contamination.R -------------------------------------------------------------------------------- /R/stats_print.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jeffsocal/tidyproteomics/HEAD/R/stats_print.R -------------------------------------------------------------------------------- /R/stats_summary.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jeffsocal/tidyproteomics/HEAD/R/stats_summary.R -------------------------------------------------------------------------------- /R/table_check.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jeffsocal/tidyproteomics/HEAD/R/table_check.R -------------------------------------------------------------------------------- /R/table_export.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jeffsocal/tidyproteomics/HEAD/R/table_export.R -------------------------------------------------------------------------------- /README.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jeffsocal/tidyproteomics/HEAD/README.md -------------------------------------------------------------------------------- /_pkgdown.yml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jeffsocal/tidyproteomics/HEAD/_pkgdown.yml -------------------------------------------------------------------------------- /data/hela_peptides.rda: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jeffsocal/tidyproteomics/HEAD/data/hela_peptides.rda -------------------------------------------------------------------------------- /data/hela_proteins.rda: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jeffsocal/tidyproteomics/HEAD/data/hela_proteins.rda -------------------------------------------------------------------------------- /docs/404.html: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jeffsocal/tidyproteomics/HEAD/docs/404.html -------------------------------------------------------------------------------- /docs/LICENSE-text.html: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jeffsocal/tidyproteomics/HEAD/docs/LICENSE-text.html -------------------------------------------------------------------------------- /docs/LICENSE.html: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jeffsocal/tidyproteomics/HEAD/docs/LICENSE.html -------------------------------------------------------------------------------- /docs/apple-touch-icon-120x120.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jeffsocal/tidyproteomics/HEAD/docs/apple-touch-icon-120x120.png -------------------------------------------------------------------------------- /docs/apple-touch-icon-152x152.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jeffsocal/tidyproteomics/HEAD/docs/apple-touch-icon-152x152.png -------------------------------------------------------------------------------- /docs/apple-touch-icon-180x180.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jeffsocal/tidyproteomics/HEAD/docs/apple-touch-icon-180x180.png -------------------------------------------------------------------------------- /docs/apple-touch-icon-60x60.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jeffsocal/tidyproteomics/HEAD/docs/apple-touch-icon-60x60.png -------------------------------------------------------------------------------- /docs/apple-touch-icon-76x76.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jeffsocal/tidyproteomics/HEAD/docs/apple-touch-icon-76x76.png -------------------------------------------------------------------------------- /docs/apple-touch-icon.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jeffsocal/tidyproteomics/HEAD/docs/apple-touch-icon.png -------------------------------------------------------------------------------- /docs/articles/annotating.html: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jeffsocal/tidyproteomics/HEAD/docs/articles/annotating.html -------------------------------------------------------------------------------- /docs/articles/annotating_files/figure-html/unnamed-chunk-11-1.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jeffsocal/tidyproteomics/HEAD/docs/articles/annotating_files/figure-html/unnamed-chunk-11-1.png -------------------------------------------------------------------------------- /docs/articles/annotating_files/figure-html/unnamed-chunk-12-1.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jeffsocal/tidyproteomics/HEAD/docs/articles/annotating_files/figure-html/unnamed-chunk-12-1.png -------------------------------------------------------------------------------- /docs/articles/automating.html: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jeffsocal/tidyproteomics/HEAD/docs/articles/automating.html -------------------------------------------------------------------------------- /docs/articles/collapsing.html: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jeffsocal/tidyproteomics/HEAD/docs/articles/collapsing.html -------------------------------------------------------------------------------- /docs/articles/collapsing_files/figure-html/unnamed-chunk-10-1.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jeffsocal/tidyproteomics/HEAD/docs/articles/collapsing_files/figure-html/unnamed-chunk-10-1.png -------------------------------------------------------------------------------- /docs/articles/collapsing_files/figure-html/unnamed-chunk-13-1.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jeffsocal/tidyproteomics/HEAD/docs/articles/collapsing_files/figure-html/unnamed-chunk-13-1.png -------------------------------------------------------------------------------- /docs/articles/collapsing_files/figure-html/unnamed-chunk-14-1.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jeffsocal/tidyproteomics/HEAD/docs/articles/collapsing_files/figure-html/unnamed-chunk-14-1.png -------------------------------------------------------------------------------- /docs/articles/collapsing_files/figure-html/unnamed-chunk-21-1.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jeffsocal/tidyproteomics/HEAD/docs/articles/collapsing_files/figure-html/unnamed-chunk-21-1.png -------------------------------------------------------------------------------- /docs/articles/collapsing_files/figure-html/unnamed-chunk-22-1.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jeffsocal/tidyproteomics/HEAD/docs/articles/collapsing_files/figure-html/unnamed-chunk-22-1.png -------------------------------------------------------------------------------- /docs/articles/collapsing_files/figure-html/unnamed-chunk-23-1.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jeffsocal/tidyproteomics/HEAD/docs/articles/collapsing_files/figure-html/unnamed-chunk-23-1.png -------------------------------------------------------------------------------- /docs/articles/collapsing_files/figure-html/unnamed-chunk-24-1.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jeffsocal/tidyproteomics/HEAD/docs/articles/collapsing_files/figure-html/unnamed-chunk-24-1.png -------------------------------------------------------------------------------- /docs/articles/collapsing_files/figure-html/unnamed-chunk-30-1.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jeffsocal/tidyproteomics/HEAD/docs/articles/collapsing_files/figure-html/unnamed-chunk-30-1.png -------------------------------------------------------------------------------- /docs/articles/collapsing_files/figure-html/unnamed-chunk-31-1.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jeffsocal/tidyproteomics/HEAD/docs/articles/collapsing_files/figure-html/unnamed-chunk-31-1.png -------------------------------------------------------------------------------- /docs/articles/collapsing_files/figure-html/unnamed-chunk-7-1.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jeffsocal/tidyproteomics/HEAD/docs/articles/collapsing_files/figure-html/unnamed-chunk-7-1.png -------------------------------------------------------------------------------- /docs/articles/collapsing_files/figure-html/unnamed-chunk-8-1.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jeffsocal/tidyproteomics/HEAD/docs/articles/collapsing_files/figure-html/unnamed-chunk-8-1.png -------------------------------------------------------------------------------- /docs/articles/data-object.html: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jeffsocal/tidyproteomics/HEAD/docs/articles/data-object.html -------------------------------------------------------------------------------- /docs/articles/enrichment.html: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jeffsocal/tidyproteomics/HEAD/docs/articles/enrichment.html -------------------------------------------------------------------------------- /docs/articles/enrichment_files/figure-html/unnamed-chunk-5-1.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jeffsocal/tidyproteomics/HEAD/docs/articles/enrichment_files/figure-html/unnamed-chunk-5-1.png -------------------------------------------------------------------------------- /docs/articles/expression.html: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jeffsocal/tidyproteomics/HEAD/docs/articles/expression.html -------------------------------------------------------------------------------- /docs/articles/expression_files/figure-html/unnamed-chunk-4-1.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jeffsocal/tidyproteomics/HEAD/docs/articles/expression_files/figure-html/unnamed-chunk-4-1.png -------------------------------------------------------------------------------- /docs/articles/expression_files/figure-html/unnamed-chunk-5-1.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jeffsocal/tidyproteomics/HEAD/docs/articles/expression_files/figure-html/unnamed-chunk-5-1.png -------------------------------------------------------------------------------- /docs/articles/expression_files/figure-html/unnamed-chunk-6-1.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jeffsocal/tidyproteomics/HEAD/docs/articles/expression_files/figure-html/unnamed-chunk-6-1.png -------------------------------------------------------------------------------- /docs/articles/expression_files/figure-html/unnamed-chunk-7-1.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jeffsocal/tidyproteomics/HEAD/docs/articles/expression_files/figure-html/unnamed-chunk-7-1.png -------------------------------------------------------------------------------- /docs/articles/expression_files/figure-html/unnamed-chunk-8-1.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jeffsocal/tidyproteomics/HEAD/docs/articles/expression_files/figure-html/unnamed-chunk-8-1.png -------------------------------------------------------------------------------- /docs/articles/expression_files/figure-html/unnamed-chunk-9-1.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jeffsocal/tidyproteomics/HEAD/docs/articles/expression_files/figure-html/unnamed-chunk-9-1.png -------------------------------------------------------------------------------- /docs/articles/extracting.html: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jeffsocal/tidyproteomics/HEAD/docs/articles/extracting.html -------------------------------------------------------------------------------- /docs/articles/extracting_files/figure-html/unnamed-chunk-3-1.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jeffsocal/tidyproteomics/HEAD/docs/articles/extracting_files/figure-html/unnamed-chunk-3-1.png -------------------------------------------------------------------------------- /docs/articles/extracting_files/figure-html/unnamed-chunk-5-1.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jeffsocal/tidyproteomics/HEAD/docs/articles/extracting_files/figure-html/unnamed-chunk-5-1.png -------------------------------------------------------------------------------- /docs/articles/images/proteins_enrichment_knockdown-control.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jeffsocal/tidyproteomics/HEAD/docs/articles/images/proteins_enrichment_knockdown-control.png -------------------------------------------------------------------------------- /docs/articles/images/uniprot_search_01.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jeffsocal/tidyproteomics/HEAD/docs/articles/images/uniprot_search_01.png -------------------------------------------------------------------------------- /docs/articles/images/uniprot_search_02.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jeffsocal/tidyproteomics/HEAD/docs/articles/images/uniprot_search_02.png -------------------------------------------------------------------------------- /docs/articles/importing.html: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jeffsocal/tidyproteomics/HEAD/docs/articles/importing.html -------------------------------------------------------------------------------- /docs/articles/imputing.html: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jeffsocal/tidyproteomics/HEAD/docs/articles/imputing.html -------------------------------------------------------------------------------- /docs/articles/imputing_files/figure-html/unnamed-chunk-5-1.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jeffsocal/tidyproteomics/HEAD/docs/articles/imputing_files/figure-html/unnamed-chunk-5-1.png -------------------------------------------------------------------------------- /docs/articles/imputing_files/figure-html/unnamed-chunk-6-1.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jeffsocal/tidyproteomics/HEAD/docs/articles/imputing_files/figure-html/unnamed-chunk-6-1.png -------------------------------------------------------------------------------- /docs/articles/imputing_files/figure-html/unnamed-chunk-8-1.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jeffsocal/tidyproteomics/HEAD/docs/articles/imputing_files/figure-html/unnamed-chunk-8-1.png -------------------------------------------------------------------------------- /docs/articles/imputing_files/figure-html/unnamed-chunk-9-1.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jeffsocal/tidyproteomics/HEAD/docs/articles/imputing_files/figure-html/unnamed-chunk-9-1.png -------------------------------------------------------------------------------- /docs/articles/index.html: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jeffsocal/tidyproteomics/HEAD/docs/articles/index.html -------------------------------------------------------------------------------- /docs/articles/normalizing.html: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jeffsocal/tidyproteomics/HEAD/docs/articles/normalizing.html -------------------------------------------------------------------------------- /docs/articles/normalizing_files/figure-html/unnamed-chunk-10-1.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jeffsocal/tidyproteomics/HEAD/docs/articles/normalizing_files/figure-html/unnamed-chunk-10-1.png -------------------------------------------------------------------------------- /docs/articles/normalizing_files/figure-html/unnamed-chunk-11-1.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jeffsocal/tidyproteomics/HEAD/docs/articles/normalizing_files/figure-html/unnamed-chunk-11-1.png -------------------------------------------------------------------------------- /docs/articles/normalizing_files/figure-html/unnamed-chunk-13-1.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jeffsocal/tidyproteomics/HEAD/docs/articles/normalizing_files/figure-html/unnamed-chunk-13-1.png -------------------------------------------------------------------------------- /docs/articles/normalizing_files/figure-html/unnamed-chunk-4-1.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jeffsocal/tidyproteomics/HEAD/docs/articles/normalizing_files/figure-html/unnamed-chunk-4-1.png -------------------------------------------------------------------------------- /docs/articles/normalizing_files/figure-html/unnamed-chunk-5-1.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jeffsocal/tidyproteomics/HEAD/docs/articles/normalizing_files/figure-html/unnamed-chunk-5-1.png -------------------------------------------------------------------------------- /docs/articles/normalizing_files/figure-html/unnamed-chunk-6-1.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jeffsocal/tidyproteomics/HEAD/docs/articles/normalizing_files/figure-html/unnamed-chunk-6-1.png -------------------------------------------------------------------------------- /docs/articles/normalizing_files/figure-html/unnamed-chunk-7-1.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jeffsocal/tidyproteomics/HEAD/docs/articles/normalizing_files/figure-html/unnamed-chunk-7-1.png -------------------------------------------------------------------------------- /docs/articles/normalizing_files/figure-html/unnamed-chunk-8-1.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jeffsocal/tidyproteomics/HEAD/docs/articles/normalizing_files/figure-html/unnamed-chunk-8-1.png -------------------------------------------------------------------------------- /docs/articles/normalizing_files/figure-html/unnamed-chunk-9-1.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jeffsocal/tidyproteomics/HEAD/docs/articles/normalizing_files/figure-html/unnamed-chunk-9-1.png -------------------------------------------------------------------------------- /docs/articles/overview.html: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jeffsocal/tidyproteomics/HEAD/docs/articles/overview.html -------------------------------------------------------------------------------- /docs/articles/proteins_enrichment_knockdown-control.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jeffsocal/tidyproteomics/HEAD/docs/articles/proteins_enrichment_knockdown-control.png -------------------------------------------------------------------------------- /docs/articles/subsetting.html: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jeffsocal/tidyproteomics/HEAD/docs/articles/subsetting.html -------------------------------------------------------------------------------- /docs/articles/summarizing.html: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jeffsocal/tidyproteomics/HEAD/docs/articles/summarizing.html -------------------------------------------------------------------------------- /docs/articles/summarizing_files/figure-html/unnamed-chunk-12-1.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jeffsocal/tidyproteomics/HEAD/docs/articles/summarizing_files/figure-html/unnamed-chunk-12-1.png -------------------------------------------------------------------------------- /docs/articles/summarizing_files/figure-html/unnamed-chunk-13-1.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jeffsocal/tidyproteomics/HEAD/docs/articles/summarizing_files/figure-html/unnamed-chunk-13-1.png -------------------------------------------------------------------------------- /docs/articles/summarizing_files/figure-html/unnamed-chunk-14-1.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jeffsocal/tidyproteomics/HEAD/docs/articles/summarizing_files/figure-html/unnamed-chunk-14-1.png -------------------------------------------------------------------------------- /docs/articles/summarizing_files/figure-html/unnamed-chunk-15-1.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jeffsocal/tidyproteomics/HEAD/docs/articles/summarizing_files/figure-html/unnamed-chunk-15-1.png -------------------------------------------------------------------------------- /docs/articles/summarizing_files/figure-html/unnamed-chunk-16-1.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jeffsocal/tidyproteomics/HEAD/docs/articles/summarizing_files/figure-html/unnamed-chunk-16-1.png -------------------------------------------------------------------------------- /docs/articles/updates.html: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jeffsocal/tidyproteomics/HEAD/docs/articles/updates.html -------------------------------------------------------------------------------- /docs/articles/visualizing.html: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jeffsocal/tidyproteomics/HEAD/docs/articles/visualizing.html -------------------------------------------------------------------------------- /docs/articles/visualizing_files/figure-html/unnamed-chunk-2-1.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jeffsocal/tidyproteomics/HEAD/docs/articles/visualizing_files/figure-html/unnamed-chunk-2-1.png -------------------------------------------------------------------------------- /docs/articles/visualizing_files/figure-html/unnamed-chunk-3-1.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jeffsocal/tidyproteomics/HEAD/docs/articles/visualizing_files/figure-html/unnamed-chunk-3-1.png -------------------------------------------------------------------------------- /docs/articles/visualizing_files/figure-html/unnamed-chunk-4-1.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jeffsocal/tidyproteomics/HEAD/docs/articles/visualizing_files/figure-html/unnamed-chunk-4-1.png -------------------------------------------------------------------------------- /docs/articles/visualizing_files/figure-html/unnamed-chunk-5-1.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jeffsocal/tidyproteomics/HEAD/docs/articles/visualizing_files/figure-html/unnamed-chunk-5-1.png -------------------------------------------------------------------------------- /docs/articles/visualizing_files/figure-html/unnamed-chunk-7-1.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jeffsocal/tidyproteomics/HEAD/docs/articles/visualizing_files/figure-html/unnamed-chunk-7-1.png -------------------------------------------------------------------------------- /docs/articles/visualizing_files/figure-html/unnamed-chunk-8-1.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jeffsocal/tidyproteomics/HEAD/docs/articles/visualizing_files/figure-html/unnamed-chunk-8-1.png -------------------------------------------------------------------------------- /docs/articles/workflow-importing.html: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jeffsocal/tidyproteomics/HEAD/docs/articles/workflow-importing.html -------------------------------------------------------------------------------- /docs/articles/workflow-publication.html: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jeffsocal/tidyproteomics/HEAD/docs/articles/workflow-publication.html -------------------------------------------------------------------------------- /docs/articles/workflow-simple.html: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jeffsocal/tidyproteomics/HEAD/docs/articles/workflow-simple.html -------------------------------------------------------------------------------- /docs/articles/workflow-userimport.html: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jeffsocal/tidyproteomics/HEAD/docs/articles/workflow-userimport.html -------------------------------------------------------------------------------- /docs/articles/workflow-userimport_files/figure-html/unnamed-chunk-10-1.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jeffsocal/tidyproteomics/HEAD/docs/articles/workflow-userimport_files/figure-html/unnamed-chunk-10-1.png -------------------------------------------------------------------------------- /docs/articles/workflow-userimport_files/figure-html/unnamed-chunk-6-1.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jeffsocal/tidyproteomics/HEAD/docs/articles/workflow-userimport_files/figure-html/unnamed-chunk-6-1.png -------------------------------------------------------------------------------- /docs/articles/workflow-userimport_files/figure-html/unnamed-chunk-7-1.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jeffsocal/tidyproteomics/HEAD/docs/articles/workflow-userimport_files/figure-html/unnamed-chunk-7-1.png -------------------------------------------------------------------------------- /docs/articles/workflow-userimport_files/figure-html/unnamed-chunk-8-1.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jeffsocal/tidyproteomics/HEAD/docs/articles/workflow-userimport_files/figure-html/unnamed-chunk-8-1.png -------------------------------------------------------------------------------- /docs/authors.html: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jeffsocal/tidyproteomics/HEAD/docs/authors.html -------------------------------------------------------------------------------- /docs/deps/bootstrap-5.1.3/bootstrap.bundle.min.js: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jeffsocal/tidyproteomics/HEAD/docs/deps/bootstrap-5.1.3/bootstrap.bundle.min.js -------------------------------------------------------------------------------- /docs/deps/bootstrap-5.1.3/bootstrap.bundle.min.js.map: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jeffsocal/tidyproteomics/HEAD/docs/deps/bootstrap-5.1.3/bootstrap.bundle.min.js.map -------------------------------------------------------------------------------- /docs/deps/bootstrap-5.1.3/bootstrap.min.css: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jeffsocal/tidyproteomics/HEAD/docs/deps/bootstrap-5.1.3/bootstrap.min.css -------------------------------------------------------------------------------- /docs/deps/bootstrap-5.2.2/bootstrap.bundle.min.js: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jeffsocal/tidyproteomics/HEAD/docs/deps/bootstrap-5.2.2/bootstrap.bundle.min.js -------------------------------------------------------------------------------- /docs/deps/bootstrap-5.2.2/bootstrap.bundle.min.js.map: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jeffsocal/tidyproteomics/HEAD/docs/deps/bootstrap-5.2.2/bootstrap.bundle.min.js.map -------------------------------------------------------------------------------- /docs/deps/bootstrap-5.2.2/bootstrap.min.css: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jeffsocal/tidyproteomics/HEAD/docs/deps/bootstrap-5.2.2/bootstrap.min.css -------------------------------------------------------------------------------- /docs/deps/bootstrap-5.3.1/bootstrap.bundle.min.js: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jeffsocal/tidyproteomics/HEAD/docs/deps/bootstrap-5.3.1/bootstrap.bundle.min.js -------------------------------------------------------------------------------- /docs/deps/bootstrap-5.3.1/bootstrap.bundle.min.js.map: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jeffsocal/tidyproteomics/HEAD/docs/deps/bootstrap-5.3.1/bootstrap.bundle.min.js.map -------------------------------------------------------------------------------- /docs/deps/bootstrap-5.3.1/bootstrap.min.css: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jeffsocal/tidyproteomics/HEAD/docs/deps/bootstrap-5.3.1/bootstrap.min.css -------------------------------------------------------------------------------- /docs/deps/bootstrap-5.3.1/font.css: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jeffsocal/tidyproteomics/HEAD/docs/deps/bootstrap-5.3.1/font.css -------------------------------------------------------------------------------- /docs/deps/bootstrap-5.3.1/fonts/1Ptxg8zYS_SKggPN4iEgvnHyvveLxVs9pbCIPrc.woff: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jeffsocal/tidyproteomics/HEAD/docs/deps/bootstrap-5.3.1/fonts/1Ptxg8zYS_SKggPN4iEgvnHyvveLxVs9pbCIPrc.woff -------------------------------------------------------------------------------- /docs/deps/bootstrap-5.3.1/fonts/1Ptxg8zYS_SKggPN4iEgvnHyvveLxVvaorCIPrc.woff: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jeffsocal/tidyproteomics/HEAD/docs/deps/bootstrap-5.3.1/fonts/1Ptxg8zYS_SKggPN4iEgvnHyvveLxVvaorCIPrc.woff -------------------------------------------------------------------------------- /docs/deps/bootstrap-5.3.1/fonts/1adeadb2fe618c5ed46221f15e12b9c8.woff: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jeffsocal/tidyproteomics/HEAD/docs/deps/bootstrap-5.3.1/fonts/1adeadb2fe618c5ed46221f15e12b9c8.woff -------------------------------------------------------------------------------- /docs/deps/bootstrap-5.3.1/fonts/4iCs6KVjbNBYlgo6ew.woff: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jeffsocal/tidyproteomics/HEAD/docs/deps/bootstrap-5.3.1/fonts/4iCs6KVjbNBYlgo6ew.woff -------------------------------------------------------------------------------- /docs/deps/bootstrap-5.3.1/fonts/4iCs6KVjbNBYlgoKfw7w.woff: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jeffsocal/tidyproteomics/HEAD/docs/deps/bootstrap-5.3.1/fonts/4iCs6KVjbNBYlgoKfw7w.woff -------------------------------------------------------------------------------- /docs/deps/bootstrap-5.3.1/fonts/4iCv6KVjbNBYlgoCxCvTtA.woff: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jeffsocal/tidyproteomics/HEAD/docs/deps/bootstrap-5.3.1/fonts/4iCv6KVjbNBYlgoCxCvTtA.woff -------------------------------------------------------------------------------- /docs/deps/bootstrap-5.3.1/fonts/4iCv6KVjbNBYlgoCxCvjsGyL.woff: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jeffsocal/tidyproteomics/HEAD/docs/deps/bootstrap-5.3.1/fonts/4iCv6KVjbNBYlgoCxCvjsGyL.woff -------------------------------------------------------------------------------- /docs/deps/bootstrap-5.3.1/fonts/6xK1dSBYKcSV-LCoeQqfX1RYOo3qPZ7nsDQ.woff: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jeffsocal/tidyproteomics/HEAD/docs/deps/bootstrap-5.3.1/fonts/6xK1dSBYKcSV-LCoeQqfX1RYOo3qPZ7nsDQ.woff -------------------------------------------------------------------------------- /docs/deps/bootstrap-5.3.1/fonts/6xK1dSBYKcSV-LCoeQqfX1RYOo3qPa7j.woff: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jeffsocal/tidyproteomics/HEAD/docs/deps/bootstrap-5.3.1/fonts/6xK1dSBYKcSV-LCoeQqfX1RYOo3qPa7j.woff -------------------------------------------------------------------------------- /docs/deps/bootstrap-5.3.1/fonts/6xK3dSBYKcSV-LCoeQqfX1RYOo3aPA.woff: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jeffsocal/tidyproteomics/HEAD/docs/deps/bootstrap-5.3.1/fonts/6xK3dSBYKcSV-LCoeQqfX1RYOo3aPA.woff -------------------------------------------------------------------------------- /docs/deps/bootstrap-5.3.1/fonts/6xK3dSBYKcSV-LCoeQqfX1RYOo3qOK7j.woff: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jeffsocal/tidyproteomics/HEAD/docs/deps/bootstrap-5.3.1/fonts/6xK3dSBYKcSV-LCoeQqfX1RYOo3qOK7j.woff -------------------------------------------------------------------------------- /docs/deps/bootstrap-5.3.1/fonts/6xKydSBYKcSV-LCoeQqfX1RYOo3i54rAkw.woff: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jeffsocal/tidyproteomics/HEAD/docs/deps/bootstrap-5.3.1/fonts/6xKydSBYKcSV-LCoeQqfX1RYOo3i54rAkw.woff -------------------------------------------------------------------------------- /docs/deps/bootstrap-5.3.1/fonts/6xKydSBYKcSV-LCoeQqfX1RYOo3ig4vAkw.woff: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jeffsocal/tidyproteomics/HEAD/docs/deps/bootstrap-5.3.1/fonts/6xKydSBYKcSV-LCoeQqfX1RYOo3ig4vAkw.woff -------------------------------------------------------------------------------- /docs/deps/bootstrap-5.3.1/fonts/6xKydSBYKcSV-LCoeQqfX1RYOo3ig4vwlxdo.woff: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jeffsocal/tidyproteomics/HEAD/docs/deps/bootstrap-5.3.1/fonts/6xKydSBYKcSV-LCoeQqfX1RYOo3ig4vwlxdo.woff -------------------------------------------------------------------------------- /docs/deps/bootstrap-5.3.1/fonts/6xKydSBYKcSV-LCoeQqfX1RYOo3ik4zAkw.woff: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jeffsocal/tidyproteomics/HEAD/docs/deps/bootstrap-5.3.1/fonts/6xKydSBYKcSV-LCoeQqfX1RYOo3ik4zAkw.woff -------------------------------------------------------------------------------- /docs/deps/bootstrap-5.3.1/fonts/6xKydSBYKcSV-LCoeQqfX1RYOo3ik4zwlxdo.woff: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jeffsocal/tidyproteomics/HEAD/docs/deps/bootstrap-5.3.1/fonts/6xKydSBYKcSV-LCoeQqfX1RYOo3ik4zwlxdo.woff -------------------------------------------------------------------------------- /docs/deps/bootstrap-5.3.1/fonts/CSR54z1Qlv-GDxkbKVQ_dFsvWNRevw.woff: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jeffsocal/tidyproteomics/HEAD/docs/deps/bootstrap-5.3.1/fonts/CSR54z1Qlv-GDxkbKVQ_dFsvWNRevw.woff -------------------------------------------------------------------------------- /docs/deps/bootstrap-5.3.1/fonts/CSR54z1Qlv-GDxkbKVQ_dFsvaNA.woff: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jeffsocal/tidyproteomics/HEAD/docs/deps/bootstrap-5.3.1/fonts/CSR54z1Qlv-GDxkbKVQ_dFsvaNA.woff -------------------------------------------------------------------------------- /docs/deps/bootstrap-5.3.1/fonts/CSR64z1Qlv-GDxkbKVQ_TOQ.woff: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jeffsocal/tidyproteomics/HEAD/docs/deps/bootstrap-5.3.1/fonts/CSR64z1Qlv-GDxkbKVQ_TOQ.woff -------------------------------------------------------------------------------- /docs/deps/bootstrap-5.3.1/fonts/CSR64z1Qlv-GDxkbKVQ_fOAKSw.woff: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jeffsocal/tidyproteomics/HEAD/docs/deps/bootstrap-5.3.1/fonts/CSR64z1Qlv-GDxkbKVQ_fOAKSw.woff -------------------------------------------------------------------------------- /docs/deps/bootstrap-5.3.1/fonts/HI_diYsKILxRpg3hIP6sJ7fM7PqPMcMnZFqUwX28DBKXhM0.woff: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jeffsocal/tidyproteomics/HEAD/docs/deps/bootstrap-5.3.1/fonts/HI_diYsKILxRpg3hIP6sJ7fM7PqPMcMnZFqUwX28DBKXhM0.woff -------------------------------------------------------------------------------- /docs/deps/bootstrap-5.3.1/fonts/HI_diYsKILxRpg3hIP6sJ7fM7PqPMcMnZFqUwX28DMyQhM0.woff: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jeffsocal/tidyproteomics/HEAD/docs/deps/bootstrap-5.3.1/fonts/HI_diYsKILxRpg3hIP6sJ7fM7PqPMcMnZFqUwX28DMyQhM0.woff -------------------------------------------------------------------------------- /docs/deps/bootstrap-5.3.1/fonts/HI_jiYsKILxRpg3hIP6sJ7fM7PqlOPHYvDP_W9O7GQTTbI1rSg.woff: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jeffsocal/tidyproteomics/HEAD/docs/deps/bootstrap-5.3.1/fonts/HI_jiYsKILxRpg3hIP6sJ7fM7PqlOPHYvDP_W9O7GQTTbI1rSg.woff -------------------------------------------------------------------------------- /docs/deps/bootstrap-5.3.1/fonts/HI_jiYsKILxRpg3hIP6sJ7fM7PqlOPHYvDP_W9O7GQTTsoprSg.woff: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jeffsocal/tidyproteomics/HEAD/docs/deps/bootstrap-5.3.1/fonts/HI_jiYsKILxRpg3hIP6sJ7fM7PqlOPHYvDP_W9O7GQTTsoprSg.woff -------------------------------------------------------------------------------- /docs/deps/bootstrap-5.3.1/fonts/JTUHjIg1_i6t8kCHKm4532VJOt5-QNFgpCtZ6Ew9.woff: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jeffsocal/tidyproteomics/HEAD/docs/deps/bootstrap-5.3.1/fonts/JTUHjIg1_i6t8kCHKm4532VJOt5-QNFgpCtZ6Ew9.woff -------------------------------------------------------------------------------- /docs/deps/bootstrap-5.3.1/fonts/JTUHjIg1_i6t8kCHKm4532VJOt5-QNFgpCtr6Ew9.woff: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jeffsocal/tidyproteomics/HEAD/docs/deps/bootstrap-5.3.1/fonts/JTUHjIg1_i6t8kCHKm4532VJOt5-QNFgpCtr6Ew9.woff -------------------------------------------------------------------------------- /docs/deps/bootstrap-5.3.1/fonts/JTUHjIg1_i6t8kCHKm4532VJOt5-QNFgpCuM70w9.woff: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jeffsocal/tidyproteomics/HEAD/docs/deps/bootstrap-5.3.1/fonts/JTUHjIg1_i6t8kCHKm4532VJOt5-QNFgpCuM70w9.woff -------------------------------------------------------------------------------- /docs/deps/bootstrap-5.3.1/fonts/KFOlCnqEu92Fr1MmEU9fBBc-.woff: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jeffsocal/tidyproteomics/HEAD/docs/deps/bootstrap-5.3.1/fonts/KFOlCnqEu92Fr1MmEU9fBBc-.woff -------------------------------------------------------------------------------- /docs/deps/bootstrap-5.3.1/fonts/KFOlCnqEu92Fr1MmEU9vAA.woff: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jeffsocal/tidyproteomics/HEAD/docs/deps/bootstrap-5.3.1/fonts/KFOlCnqEu92Fr1MmEU9vAA.woff -------------------------------------------------------------------------------- /docs/deps/bootstrap-5.3.1/fonts/KFOlCnqEu92Fr1MmSU5fBBc-.woff: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jeffsocal/tidyproteomics/HEAD/docs/deps/bootstrap-5.3.1/fonts/KFOlCnqEu92Fr1MmSU5fBBc-.woff -------------------------------------------------------------------------------- /docs/deps/bootstrap-5.3.1/fonts/KFOlCnqEu92Fr1MmSU5vAA.woff: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jeffsocal/tidyproteomics/HEAD/docs/deps/bootstrap-5.3.1/fonts/KFOlCnqEu92Fr1MmSU5vAA.woff -------------------------------------------------------------------------------- /docs/deps/bootstrap-5.3.1/fonts/KFOlCnqEu92Fr1MmWUlfBBc-.woff: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jeffsocal/tidyproteomics/HEAD/docs/deps/bootstrap-5.3.1/fonts/KFOlCnqEu92Fr1MmWUlfBBc-.woff -------------------------------------------------------------------------------- /docs/deps/bootstrap-5.3.1/fonts/KFOlCnqEu92Fr1MmWUlvAA.woff: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jeffsocal/tidyproteomics/HEAD/docs/deps/bootstrap-5.3.1/fonts/KFOlCnqEu92Fr1MmWUlvAA.woff -------------------------------------------------------------------------------- /docs/deps/bootstrap-5.3.1/fonts/KFOmCnqEu92Fr1Me5g.woff: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jeffsocal/tidyproteomics/HEAD/docs/deps/bootstrap-5.3.1/fonts/KFOmCnqEu92Fr1Me5g.woff -------------------------------------------------------------------------------- /docs/deps/bootstrap-5.3.1/fonts/KFOmCnqEu92Fr1Mu4mxM.woff: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jeffsocal/tidyproteomics/HEAD/docs/deps/bootstrap-5.3.1/fonts/KFOmCnqEu92Fr1Mu4mxM.woff -------------------------------------------------------------------------------- /docs/deps/bootstrap-5.3.1/fonts/QGYpz_kZZAGCONcK2A4bGOj8mNhL.woff: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jeffsocal/tidyproteomics/HEAD/docs/deps/bootstrap-5.3.1/fonts/QGYpz_kZZAGCONcK2A4bGOj8mNhL.woff -------------------------------------------------------------------------------- /docs/deps/bootstrap-5.3.1/fonts/S6u8w4BMUTPHjxsAXC-s.woff: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jeffsocal/tidyproteomics/HEAD/docs/deps/bootstrap-5.3.1/fonts/S6u8w4BMUTPHjxsAXC-s.woff -------------------------------------------------------------------------------- /docs/deps/bootstrap-5.3.1/fonts/S6u8w4BMUTPHjxswWA.woff: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jeffsocal/tidyproteomics/HEAD/docs/deps/bootstrap-5.3.1/fonts/S6u8w4BMUTPHjxswWA.woff -------------------------------------------------------------------------------- /docs/deps/bootstrap-5.3.1/fonts/S6u9w4BMUTPHh6UVSwiPHw.woff: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jeffsocal/tidyproteomics/HEAD/docs/deps/bootstrap-5.3.1/fonts/S6u9w4BMUTPHh6UVSwiPHw.woff -------------------------------------------------------------------------------- /docs/deps/bootstrap-5.3.1/fonts/S6u9w4BMUTPHh6UVeww.woff: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jeffsocal/tidyproteomics/HEAD/docs/deps/bootstrap-5.3.1/fonts/S6u9w4BMUTPHh6UVeww.woff -------------------------------------------------------------------------------- /docs/deps/bootstrap-5.3.1/fonts/S6u9w4BMUTPHh7USSwiPHw.woff: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jeffsocal/tidyproteomics/HEAD/docs/deps/bootstrap-5.3.1/fonts/S6u9w4BMUTPHh7USSwiPHw.woff -------------------------------------------------------------------------------- /docs/deps/bootstrap-5.3.1/fonts/S6u9w4BMUTPHh7USeww.woff: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jeffsocal/tidyproteomics/HEAD/docs/deps/bootstrap-5.3.1/fonts/S6u9w4BMUTPHh7USeww.woff -------------------------------------------------------------------------------- /docs/deps/bootstrap-5.3.1/fonts/S6uyw4BMUTPHjx4wWA.woff: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jeffsocal/tidyproteomics/HEAD/docs/deps/bootstrap-5.3.1/fonts/S6uyw4BMUTPHjx4wWA.woff -------------------------------------------------------------------------------- /docs/deps/bootstrap-5.3.1/fonts/S6uyw4BMUTPHvxo.woff: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jeffsocal/tidyproteomics/HEAD/docs/deps/bootstrap-5.3.1/fonts/S6uyw4BMUTPHvxo.woff -------------------------------------------------------------------------------- /docs/deps/bootstrap-5.3.1/fonts/UcCO3FwrK3iLTeHuS_fvQtMwCp50KnMw2boKoduKmMEVuFuYMZs.woff: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jeffsocal/tidyproteomics/HEAD/docs/deps/bootstrap-5.3.1/fonts/UcCO3FwrK3iLTeHuS_fvQtMwCp50KnMw2boKoduKmMEVuFuYMZs.woff -------------------------------------------------------------------------------- /docs/deps/bootstrap-5.3.1/fonts/UcCO3FwrK3iLTeHuS_fvQtMwCp50KnMw2boKoduKmMEVuI6fMZs.woff: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jeffsocal/tidyproteomics/HEAD/docs/deps/bootstrap-5.3.1/fonts/UcCO3FwrK3iLTeHuS_fvQtMwCp50KnMw2boKoduKmMEVuI6fMZs.woff -------------------------------------------------------------------------------- /docs/deps/bootstrap-5.3.1/fonts/UcCO3FwrK3iLTeHuS_fvQtMwCp50KnMw2boKoduKmMEVuLyfMZs.woff: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jeffsocal/tidyproteomics/HEAD/docs/deps/bootstrap-5.3.1/fonts/UcCO3FwrK3iLTeHuS_fvQtMwCp50KnMw2boKoduKmMEVuLyfMZs.woff -------------------------------------------------------------------------------- /docs/deps/bootstrap-5.3.1/fonts/XRXI3I6Li01BKofiOc5wtlZ2di8HDFwmRTA.woff: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jeffsocal/tidyproteomics/HEAD/docs/deps/bootstrap-5.3.1/fonts/XRXI3I6Li01BKofiOc5wtlZ2di8HDFwmRTA.woff -------------------------------------------------------------------------------- /docs/deps/bootstrap-5.3.1/fonts/XRXI3I6Li01BKofiOc5wtlZ2di8HDGUmRTA.woff: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jeffsocal/tidyproteomics/HEAD/docs/deps/bootstrap-5.3.1/fonts/XRXI3I6Li01BKofiOc5wtlZ2di8HDGUmRTA.woff -------------------------------------------------------------------------------- /docs/deps/bootstrap-5.3.1/fonts/XRXI3I6Li01BKofiOc5wtlZ2di8HDLshRTA.woff: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jeffsocal/tidyproteomics/HEAD/docs/deps/bootstrap-5.3.1/fonts/XRXI3I6Li01BKofiOc5wtlZ2di8HDLshRTA.woff -------------------------------------------------------------------------------- /docs/deps/bootstrap-5.3.1/fonts/a98f7a7574819ba83bec6279a2cecd95.woff: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jeffsocal/tidyproteomics/HEAD/docs/deps/bootstrap-5.3.1/fonts/a98f7a7574819ba83bec6279a2cecd95.woff -------------------------------------------------------------------------------- /docs/deps/bootstrap-5.3.1/fonts/memQYaGs126MiZpBA-UFUIcVXSCEkx2cmqvXlWq8tWZ0Pw86hd0Rk0ZjaVQ.woff: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jeffsocal/tidyproteomics/HEAD/docs/deps/bootstrap-5.3.1/fonts/memQYaGs126MiZpBA-UFUIcVXSCEkx2cmqvXlWq8tWZ0Pw86hd0Rk0ZjaVQ.woff -------------------------------------------------------------------------------- /docs/deps/bootstrap-5.3.1/fonts/memQYaGs126MiZpBA-UFUIcVXSCEkx2cmqvXlWq8tWZ0Pw86hd0Rk5hkWVAexg.woff: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jeffsocal/tidyproteomics/HEAD/docs/deps/bootstrap-5.3.1/fonts/memQYaGs126MiZpBA-UFUIcVXSCEkx2cmqvXlWq8tWZ0Pw86hd0Rk5hkWVAexg.woff -------------------------------------------------------------------------------- /docs/deps/bootstrap-5.3.1/fonts/memQYaGs126MiZpBA-UFUIcVXSCEkx2cmqvXlWq8tWZ0Pw86hd0Rk5hkaVQ.woff: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jeffsocal/tidyproteomics/HEAD/docs/deps/bootstrap-5.3.1/fonts/memQYaGs126MiZpBA-UFUIcVXSCEkx2cmqvXlWq8tWZ0Pw86hd0Rk5hkaVQ.woff -------------------------------------------------------------------------------- /docs/deps/bootstrap-5.3.1/fonts/memQYaGs126MiZpBA-UFUIcVXSCEkx2cmqvXlWq8tWZ0Pw86hd0Rk8ZkWVAexg.woff: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jeffsocal/tidyproteomics/HEAD/docs/deps/bootstrap-5.3.1/fonts/memQYaGs126MiZpBA-UFUIcVXSCEkx2cmqvXlWq8tWZ0Pw86hd0Rk8ZkWVAexg.woff -------------------------------------------------------------------------------- /docs/deps/bootstrap-5.3.1/fonts/memQYaGs126MiZpBA-UFUIcVXSCEkx2cmqvXlWq8tWZ0Pw86hd0Rk8ZkaVQ.woff: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jeffsocal/tidyproteomics/HEAD/docs/deps/bootstrap-5.3.1/fonts/memQYaGs126MiZpBA-UFUIcVXSCEkx2cmqvXlWq8tWZ0Pw86hd0Rk8ZkaVQ.woff -------------------------------------------------------------------------------- /docs/deps/bootstrap-5.3.1/fonts/memQYaGs126MiZpBA-UFUIcVXSCEkx2cmqvXlWq8tWZ0Pw86hd0Rk_RkaVQ.woff: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jeffsocal/tidyproteomics/HEAD/docs/deps/bootstrap-5.3.1/fonts/memQYaGs126MiZpBA-UFUIcVXSCEkx2cmqvXlWq8tWZ0Pw86hd0Rk_RkaVQ.woff -------------------------------------------------------------------------------- /docs/deps/bootstrap-5.3.1/fonts/memQYaGs126MiZpBA-UFUIcVXSCEkx2cmqvXlWq8tWZ0Pw86hd0RkxhjaVQ.woff: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jeffsocal/tidyproteomics/HEAD/docs/deps/bootstrap-5.3.1/fonts/memQYaGs126MiZpBA-UFUIcVXSCEkx2cmqvXlWq8tWZ0Pw86hd0RkxhjaVQ.woff -------------------------------------------------------------------------------- /docs/deps/bootstrap-5.3.1/fonts/memQYaGs126MiZpBA-UFUIcVXSCEkx2cmqvXlWq8tWZ0Pw86hd0RkyFjWVAexg.woff: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jeffsocal/tidyproteomics/HEAD/docs/deps/bootstrap-5.3.1/fonts/memQYaGs126MiZpBA-UFUIcVXSCEkx2cmqvXlWq8tWZ0Pw86hd0RkyFjWVAexg.woff -------------------------------------------------------------------------------- /docs/deps/bootstrap-5.3.1/fonts/memQYaGs126MiZpBA-UFUIcVXSCEkx2cmqvXlWq8tWZ0Pw86hd0RkyFjaVQ.woff: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jeffsocal/tidyproteomics/HEAD/docs/deps/bootstrap-5.3.1/fonts/memQYaGs126MiZpBA-UFUIcVXSCEkx2cmqvXlWq8tWZ0Pw86hd0RkyFjaVQ.woff -------------------------------------------------------------------------------- /docs/deps/bootstrap-5.3.1/fonts/memSYaGs126MiZpBA-UvWbX2vVnXBbObj2OVZyOOSr4dVJWUgsg-1x4gaVQ.woff: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jeffsocal/tidyproteomics/HEAD/docs/deps/bootstrap-5.3.1/fonts/memSYaGs126MiZpBA-UvWbX2vVnXBbObj2OVZyOOSr4dVJWUgsg-1x4gaVQ.woff -------------------------------------------------------------------------------- /docs/deps/bootstrap-5.3.1/fonts/memSYaGs126MiZpBA-UvWbX2vVnXBbObj2OVZyOOSr4dVJWUgsg-1y4k.woff: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jeffsocal/tidyproteomics/HEAD/docs/deps/bootstrap-5.3.1/fonts/memSYaGs126MiZpBA-UvWbX2vVnXBbObj2OVZyOOSr4dVJWUgsg-1y4k.woff -------------------------------------------------------------------------------- /docs/deps/bootstrap-5.3.1/fonts/memSYaGs126MiZpBA-UvWbX2vVnXBbObj2OVZyOOSr4dVJWUgsgH1y4k.woff: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jeffsocal/tidyproteomics/HEAD/docs/deps/bootstrap-5.3.1/fonts/memSYaGs126MiZpBA-UvWbX2vVnXBbObj2OVZyOOSr4dVJWUgsgH1y4k.woff -------------------------------------------------------------------------------- /docs/deps/bootstrap-5.3.1/fonts/memSYaGs126MiZpBA-UvWbX2vVnXBbObj2OVZyOOSr4dVJWUgshZ1y4k.woff: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jeffsocal/tidyproteomics/HEAD/docs/deps/bootstrap-5.3.1/fonts/memSYaGs126MiZpBA-UvWbX2vVnXBbObj2OVZyOOSr4dVJWUgshZ1y4k.woff -------------------------------------------------------------------------------- /docs/deps/bootstrap-5.3.1/fonts/memSYaGs126MiZpBA-UvWbX2vVnXBbObj2OVZyOOSr4dVJWUgsiH0B4gaVQ.woff: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jeffsocal/tidyproteomics/HEAD/docs/deps/bootstrap-5.3.1/fonts/memSYaGs126MiZpBA-UvWbX2vVnXBbObj2OVZyOOSr4dVJWUgsiH0B4gaVQ.woff -------------------------------------------------------------------------------- /docs/deps/bootstrap-5.3.1/fonts/memSYaGs126MiZpBA-UvWbX2vVnXBbObj2OVZyOOSr4dVJWUgsiH0C4k.woff: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jeffsocal/tidyproteomics/HEAD/docs/deps/bootstrap-5.3.1/fonts/memSYaGs126MiZpBA-UvWbX2vVnXBbObj2OVZyOOSr4dVJWUgsiH0C4k.woff -------------------------------------------------------------------------------- /docs/deps/bootstrap-5.3.1/fonts/memSYaGs126MiZpBA-UvWbX2vVnXBbObj2OVZyOOSr4dVJWUgsjZ0B4gaVQ.woff: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jeffsocal/tidyproteomics/HEAD/docs/deps/bootstrap-5.3.1/fonts/memSYaGs126MiZpBA-UvWbX2vVnXBbObj2OVZyOOSr4dVJWUgsjZ0B4gaVQ.woff -------------------------------------------------------------------------------- /docs/deps/bootstrap-5.3.1/fonts/memSYaGs126MiZpBA-UvWbX2vVnXBbObj2OVZyOOSr4dVJWUgsjZ0C4k.woff: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jeffsocal/tidyproteomics/HEAD/docs/deps/bootstrap-5.3.1/fonts/memSYaGs126MiZpBA-UvWbX2vVnXBbObj2OVZyOOSr4dVJWUgsjZ0C4k.woff -------------------------------------------------------------------------------- /docs/deps/bootstrap-5.3.1/fonts/memSYaGs126MiZpBA-UvWbX2vVnXBbObj2OVZyOOSr4dVJWUgsjr0C4k.woff: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jeffsocal/tidyproteomics/HEAD/docs/deps/bootstrap-5.3.1/fonts/memSYaGs126MiZpBA-UvWbX2vVnXBbObj2OVZyOOSr4dVJWUgsjr0C4k.woff -------------------------------------------------------------------------------- /docs/deps/bootstrap-5.3.1/fonts/q5uGsou0JOdh94bfvQlr.woff: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jeffsocal/tidyproteomics/HEAD/docs/deps/bootstrap-5.3.1/fonts/q5uGsou0JOdh94bfvQlr.woff -------------------------------------------------------------------------------- /docs/deps/data-deps.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jeffsocal/tidyproteomics/HEAD/docs/deps/data-deps.txt -------------------------------------------------------------------------------- /docs/deps/jquery-3.6.0/jquery-3.6.0.js: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jeffsocal/tidyproteomics/HEAD/docs/deps/jquery-3.6.0/jquery-3.6.0.js -------------------------------------------------------------------------------- /docs/deps/jquery-3.6.0/jquery-3.6.0.min.js: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jeffsocal/tidyproteomics/HEAD/docs/deps/jquery-3.6.0/jquery-3.6.0.min.js -------------------------------------------------------------------------------- /docs/deps/jquery-3.6.0/jquery-3.6.0.min.map: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jeffsocal/tidyproteomics/HEAD/docs/deps/jquery-3.6.0/jquery-3.6.0.min.map -------------------------------------------------------------------------------- /docs/favicon-16x16.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jeffsocal/tidyproteomics/HEAD/docs/favicon-16x16.png -------------------------------------------------------------------------------- /docs/favicon-32x32.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jeffsocal/tidyproteomics/HEAD/docs/favicon-32x32.png -------------------------------------------------------------------------------- /docs/favicon.ico: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jeffsocal/tidyproteomics/HEAD/docs/favicon.ico -------------------------------------------------------------------------------- /docs/images/uniprot_search_01.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jeffsocal/tidyproteomics/HEAD/docs/images/uniprot_search_01.png -------------------------------------------------------------------------------- /docs/images/uniprot_search_02.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jeffsocal/tidyproteomics/HEAD/docs/images/uniprot_search_02.png -------------------------------------------------------------------------------- /docs/index.html: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jeffsocal/tidyproteomics/HEAD/docs/index.html -------------------------------------------------------------------------------- /docs/link.svg: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jeffsocal/tidyproteomics/HEAD/docs/link.svg -------------------------------------------------------------------------------- /docs/logo.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jeffsocal/tidyproteomics/HEAD/docs/logo.png -------------------------------------------------------------------------------- /docs/pkgdown.js: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jeffsocal/tidyproteomics/HEAD/docs/pkgdown.js -------------------------------------------------------------------------------- /docs/pkgdown.yml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jeffsocal/tidyproteomics/HEAD/docs/pkgdown.yml -------------------------------------------------------------------------------- /docs/reference/Rplot001.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jeffsocal/tidyproteomics/HEAD/docs/reference/Rplot001.png -------------------------------------------------------------------------------- /docs/reference/Rplot002.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jeffsocal/tidyproteomics/HEAD/docs/reference/Rplot002.png -------------------------------------------------------------------------------- /docs/reference/Rplot003.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jeffsocal/tidyproteomics/HEAD/docs/reference/Rplot003.png -------------------------------------------------------------------------------- /docs/reference/Rplot004.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jeffsocal/tidyproteomics/HEAD/docs/reference/Rplot004.png -------------------------------------------------------------------------------- /docs/reference/align_modification.html: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jeffsocal/tidyproteomics/HEAD/docs/reference/align_modification.html -------------------------------------------------------------------------------- /docs/reference/align_peptide.html: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jeffsocal/tidyproteomics/HEAD/docs/reference/align_peptide.html -------------------------------------------------------------------------------- /docs/reference/analysis_counts.html: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jeffsocal/tidyproteomics/HEAD/docs/reference/analysis_counts.html -------------------------------------------------------------------------------- /docs/reference/analyze_enrichments.html: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jeffsocal/tidyproteomics/HEAD/docs/reference/analyze_enrichments.html -------------------------------------------------------------------------------- /docs/reference/analyze_expressions.html: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jeffsocal/tidyproteomics/HEAD/docs/reference/analyze_expressions.html -------------------------------------------------------------------------------- /docs/reference/annotate.html: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jeffsocal/tidyproteomics/HEAD/docs/reference/annotate.html -------------------------------------------------------------------------------- /docs/reference/as.data.frame.tidyproteomics.html: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jeffsocal/tidyproteomics/HEAD/docs/reference/as.data.frame.tidyproteomics.html -------------------------------------------------------------------------------- /docs/reference/calc_enrichment.html: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jeffsocal/tidyproteomics/HEAD/docs/reference/calc_enrichment.html -------------------------------------------------------------------------------- /docs/reference/center.html: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jeffsocal/tidyproteomics/HEAD/docs/reference/center.html -------------------------------------------------------------------------------- /docs/reference/check_data.html: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jeffsocal/tidyproteomics/HEAD/docs/reference/check_data.html -------------------------------------------------------------------------------- /docs/reference/check_pairs.html: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jeffsocal/tidyproteomics/HEAD/docs/reference/check_pairs.html -------------------------------------------------------------------------------- /docs/reference/check_table.html: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jeffsocal/tidyproteomics/HEAD/docs/reference/check_table.html -------------------------------------------------------------------------------- /docs/reference/codify.html: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jeffsocal/tidyproteomics/HEAD/docs/reference/codify.html -------------------------------------------------------------------------------- /docs/reference/collapse.html: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jeffsocal/tidyproteomics/HEAD/docs/reference/collapse.html -------------------------------------------------------------------------------- /docs/reference/compute_compexp.html: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jeffsocal/tidyproteomics/HEAD/docs/reference/compute_compexp.html -------------------------------------------------------------------------------- /docs/reference/data_import.html: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jeffsocal/tidyproteomics/HEAD/docs/reference/data_import.html -------------------------------------------------------------------------------- /docs/reference/down_select.html: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jeffsocal/tidyproteomics/HEAD/docs/reference/down_select.html -------------------------------------------------------------------------------- /docs/reference/enrichment.html: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jeffsocal/tidyproteomics/HEAD/docs/reference/enrichment.html -------------------------------------------------------------------------------- /docs/reference/enrichment_fishersexact.html: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jeffsocal/tidyproteomics/HEAD/docs/reference/enrichment_fishersexact.html -------------------------------------------------------------------------------- /docs/reference/enrichment_gsea.html: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jeffsocal/tidyproteomics/HEAD/docs/reference/enrichment_gsea.html -------------------------------------------------------------------------------- /docs/reference/enrichment_wilcoxon.html: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jeffsocal/tidyproteomics/HEAD/docs/reference/enrichment_wilcoxon.html -------------------------------------------------------------------------------- /docs/reference/experimental.html: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jeffsocal/tidyproteomics/HEAD/docs/reference/experimental.html -------------------------------------------------------------------------------- /docs/reference/experimental_groups.html: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jeffsocal/tidyproteomics/HEAD/docs/reference/experimental_groups.html -------------------------------------------------------------------------------- /docs/reference/export_analysis.html: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jeffsocal/tidyproteomics/HEAD/docs/reference/export_analysis.html -------------------------------------------------------------------------------- /docs/reference/export_compexp.html: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jeffsocal/tidyproteomics/HEAD/docs/reference/export_compexp.html -------------------------------------------------------------------------------- /docs/reference/export_config.html: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jeffsocal/tidyproteomics/HEAD/docs/reference/export_config.html -------------------------------------------------------------------------------- /docs/reference/export_quant.html: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jeffsocal/tidyproteomics/HEAD/docs/reference/export_quant.html -------------------------------------------------------------------------------- /docs/reference/expression.html: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jeffsocal/tidyproteomics/HEAD/docs/reference/expression.html -------------------------------------------------------------------------------- /docs/reference/expression_limma.html: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jeffsocal/tidyproteomics/HEAD/docs/reference/expression_limma.html -------------------------------------------------------------------------------- /docs/reference/expression_test.html: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jeffsocal/tidyproteomics/HEAD/docs/reference/expression_test.html -------------------------------------------------------------------------------- /docs/reference/extract.html: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jeffsocal/tidyproteomics/HEAD/docs/reference/extract.html -------------------------------------------------------------------------------- /docs/reference/fasta_digest.html: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jeffsocal/tidyproteomics/HEAD/docs/reference/fasta_digest.html -------------------------------------------------------------------------------- /docs/reference/fasta_extract.html: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jeffsocal/tidyproteomics/HEAD/docs/reference/fasta_extract.html -------------------------------------------------------------------------------- /docs/reference/fasta_parse.html: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jeffsocal/tidyproteomics/HEAD/docs/reference/fasta_parse.html -------------------------------------------------------------------------------- /docs/reference/fasta_peptides.html: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jeffsocal/tidyproteomics/HEAD/docs/reference/fasta_peptides.html -------------------------------------------------------------------------------- /docs/reference/fasta_regex.html: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jeffsocal/tidyproteomics/HEAD/docs/reference/fasta_regex.html -------------------------------------------------------------------------------- /docs/reference/fgeomean.html: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jeffsocal/tidyproteomics/HEAD/docs/reference/fgeomean.html -------------------------------------------------------------------------------- /docs/reference/figures/logo.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jeffsocal/tidyproteomics/HEAD/docs/reference/figures/logo.png -------------------------------------------------------------------------------- /docs/reference/fmean.html: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jeffsocal/tidyproteomics/HEAD/docs/reference/fmean.html -------------------------------------------------------------------------------- /docs/reference/fmedian.html: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jeffsocal/tidyproteomics/HEAD/docs/reference/fmedian.html -------------------------------------------------------------------------------- /docs/reference/fmin.html: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jeffsocal/tidyproteomics/HEAD/docs/reference/fmin.html -------------------------------------------------------------------------------- /docs/reference/fsum.html: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jeffsocal/tidyproteomics/HEAD/docs/reference/fsum.html -------------------------------------------------------------------------------- /docs/reference/get_accountings.html: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jeffsocal/tidyproteomics/HEAD/docs/reference/get_accountings.html -------------------------------------------------------------------------------- /docs/reference/get_annotation_terms.html: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jeffsocal/tidyproteomics/HEAD/docs/reference/get_annotation_terms.html -------------------------------------------------------------------------------- /docs/reference/get_annotations.html: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jeffsocal/tidyproteomics/HEAD/docs/reference/get_annotations.html -------------------------------------------------------------------------------- /docs/reference/get_quant_names.html: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jeffsocal/tidyproteomics/HEAD/docs/reference/get_quant_names.html -------------------------------------------------------------------------------- /docs/reference/get_sample_names.html: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jeffsocal/tidyproteomics/HEAD/docs/reference/get_sample_names.html -------------------------------------------------------------------------------- /docs/reference/get_segment.html: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jeffsocal/tidyproteomics/HEAD/docs/reference/get_segment.html -------------------------------------------------------------------------------- /docs/reference/get_unique_variables.html: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jeffsocal/tidyproteomics/HEAD/docs/reference/get_unique_variables.html -------------------------------------------------------------------------------- /docs/reference/get_variables.html: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jeffsocal/tidyproteomics/HEAD/docs/reference/get_variables.html -------------------------------------------------------------------------------- /docs/reference/grapes-like-grapes.html: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jeffsocal/tidyproteomics/HEAD/docs/reference/grapes-like-grapes.html -------------------------------------------------------------------------------- /docs/reference/hash_vector.html: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jeffsocal/tidyproteomics/HEAD/docs/reference/hash_vector.html -------------------------------------------------------------------------------- /docs/reference/hdf.html: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jeffsocal/tidyproteomics/HEAD/docs/reference/hdf.html -------------------------------------------------------------------------------- /docs/reference/hela_peptides.html: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jeffsocal/tidyproteomics/HEAD/docs/reference/hela_peptides.html -------------------------------------------------------------------------------- /docs/reference/hela_proteins.html: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jeffsocal/tidyproteomics/HEAD/docs/reference/hela_proteins.html -------------------------------------------------------------------------------- /docs/reference/import.html: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jeffsocal/tidyproteomics/HEAD/docs/reference/import.html -------------------------------------------------------------------------------- /docs/reference/import_charge.html: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jeffsocal/tidyproteomics/HEAD/docs/reference/import_charge.html -------------------------------------------------------------------------------- /docs/reference/import_extract.html: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jeffsocal/tidyproteomics/HEAD/docs/reference/import_extract.html -------------------------------------------------------------------------------- /docs/reference/import_mbr.html: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jeffsocal/tidyproteomics/HEAD/docs/reference/import_mbr.html -------------------------------------------------------------------------------- /docs/reference/import_remove.html: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jeffsocal/tidyproteomics/HEAD/docs/reference/import_remove.html -------------------------------------------------------------------------------- /docs/reference/import_rename.html: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jeffsocal/tidyproteomics/HEAD/docs/reference/import_rename.html -------------------------------------------------------------------------------- /docs/reference/import_split.html: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jeffsocal/tidyproteomics/HEAD/docs/reference/import_split.html -------------------------------------------------------------------------------- /docs/reference/import_validate.html: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jeffsocal/tidyproteomics/HEAD/docs/reference/import_validate.html -------------------------------------------------------------------------------- /docs/reference/impute.html: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jeffsocal/tidyproteomics/HEAD/docs/reference/impute.html -------------------------------------------------------------------------------- /docs/reference/impute.randomforest.html: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jeffsocal/tidyproteomics/HEAD/docs/reference/impute.randomforest.html -------------------------------------------------------------------------------- /docs/reference/impute_byfunction.html: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jeffsocal/tidyproteomics/HEAD/docs/reference/impute_byfunction.html -------------------------------------------------------------------------------- /docs/reference/impute_randomforest.html: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jeffsocal/tidyproteomics/HEAD/docs/reference/impute_randomforest.html -------------------------------------------------------------------------------- /docs/reference/impute_ratio.html: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jeffsocal/tidyproteomics/HEAD/docs/reference/impute_ratio.html -------------------------------------------------------------------------------- /docs/reference/index.html: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jeffsocal/tidyproteomics/HEAD/docs/reference/index.html -------------------------------------------------------------------------------- /docs/reference/intersect_venn.html: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jeffsocal/tidyproteomics/HEAD/docs/reference/intersect_venn.html -------------------------------------------------------------------------------- /docs/reference/intersection.html: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jeffsocal/tidyproteomics/HEAD/docs/reference/intersection.html -------------------------------------------------------------------------------- /docs/reference/invlog2.html: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jeffsocal/tidyproteomics/HEAD/docs/reference/invlog2.html -------------------------------------------------------------------------------- /docs/reference/list_venn.html: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jeffsocal/tidyproteomics/HEAD/docs/reference/list_venn.html -------------------------------------------------------------------------------- /docs/reference/load_local.html: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jeffsocal/tidyproteomics/HEAD/docs/reference/load_local.html -------------------------------------------------------------------------------- /docs/reference/match_vect.html: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jeffsocal/tidyproteomics/HEAD/docs/reference/match_vect.html -------------------------------------------------------------------------------- /docs/reference/meld.html: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jeffsocal/tidyproteomics/HEAD/docs/reference/meld.html -------------------------------------------------------------------------------- /docs/reference/merge.html: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jeffsocal/tidyproteomics/HEAD/docs/reference/merge.html -------------------------------------------------------------------------------- /docs/reference/merge.tidyproteomics.html: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jeffsocal/tidyproteomics/HEAD/docs/reference/merge.tidyproteomics.html -------------------------------------------------------------------------------- /docs/reference/merge_quantitative.html: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jeffsocal/tidyproteomics/HEAD/docs/reference/merge_quantitative.html -------------------------------------------------------------------------------- /docs/reference/munge_identifier.html: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jeffsocal/tidyproteomics/HEAD/docs/reference/munge_identifier.html -------------------------------------------------------------------------------- /docs/reference/normalize.html: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jeffsocal/tidyproteomics/HEAD/docs/reference/normalize.html -------------------------------------------------------------------------------- /docs/reference/normalize_limma.html: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jeffsocal/tidyproteomics/HEAD/docs/reference/normalize_limma.html -------------------------------------------------------------------------------- /docs/reference/normalize_linear.html: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jeffsocal/tidyproteomics/HEAD/docs/reference/normalize_linear.html -------------------------------------------------------------------------------- /docs/reference/normalize_loess.html: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jeffsocal/tidyproteomics/HEAD/docs/reference/normalize_loess.html -------------------------------------------------------------------------------- /docs/reference/normalize_median.html: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jeffsocal/tidyproteomics/HEAD/docs/reference/normalize_median.html -------------------------------------------------------------------------------- /docs/reference/normalize_randomforest.html: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jeffsocal/tidyproteomics/HEAD/docs/reference/normalize_randomforest.html -------------------------------------------------------------------------------- /docs/reference/normalize_scaled.html: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jeffsocal/tidyproteomics/HEAD/docs/reference/normalize_scaled.html -------------------------------------------------------------------------------- /docs/reference/normalize_svm.html: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jeffsocal/tidyproteomics/HEAD/docs/reference/normalize_svm.html -------------------------------------------------------------------------------- /docs/reference/operations.html: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jeffsocal/tidyproteomics/HEAD/docs/reference/operations.html -------------------------------------------------------------------------------- /docs/reference/path_to_package_data.html: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jeffsocal/tidyproteomics/HEAD/docs/reference/path_to_package_data.html -------------------------------------------------------------------------------- /docs/reference/plot.tidyproteomics.html: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jeffsocal/tidyproteomics/HEAD/docs/reference/plot.tidyproteomics.html -------------------------------------------------------------------------------- /docs/reference/plot_compexp-1.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jeffsocal/tidyproteomics/HEAD/docs/reference/plot_compexp-1.png -------------------------------------------------------------------------------- /docs/reference/plot_compexp.html: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jeffsocal/tidyproteomics/HEAD/docs/reference/plot_compexp.html -------------------------------------------------------------------------------- /docs/reference/plot_counts-1.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jeffsocal/tidyproteomics/HEAD/docs/reference/plot_counts-1.png -------------------------------------------------------------------------------- /docs/reference/plot_counts-2.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jeffsocal/tidyproteomics/HEAD/docs/reference/plot_counts-2.png -------------------------------------------------------------------------------- /docs/reference/plot_counts.html: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jeffsocal/tidyproteomics/HEAD/docs/reference/plot_counts.html -------------------------------------------------------------------------------- /docs/reference/plot_dynamic_range-1.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jeffsocal/tidyproteomics/HEAD/docs/reference/plot_dynamic_range-1.png -------------------------------------------------------------------------------- /docs/reference/plot_dynamic_range.html: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jeffsocal/tidyproteomics/HEAD/docs/reference/plot_dynamic_range.html -------------------------------------------------------------------------------- /docs/reference/plot_enrichment-1.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jeffsocal/tidyproteomics/HEAD/docs/reference/plot_enrichment-1.png -------------------------------------------------------------------------------- /docs/reference/plot_enrichment.html: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jeffsocal/tidyproteomics/HEAD/docs/reference/plot_enrichment.html -------------------------------------------------------------------------------- /docs/reference/plot_euler-1.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jeffsocal/tidyproteomics/HEAD/docs/reference/plot_euler-1.png -------------------------------------------------------------------------------- /docs/reference/plot_euler-2.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jeffsocal/tidyproteomics/HEAD/docs/reference/plot_euler-2.png -------------------------------------------------------------------------------- /docs/reference/plot_euler.html: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jeffsocal/tidyproteomics/HEAD/docs/reference/plot_euler.html -------------------------------------------------------------------------------- /docs/reference/plot_heatmap.html: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jeffsocal/tidyproteomics/HEAD/docs/reference/plot_heatmap.html -------------------------------------------------------------------------------- /docs/reference/plot_normalization-1.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jeffsocal/tidyproteomics/HEAD/docs/reference/plot_normalization-1.png -------------------------------------------------------------------------------- /docs/reference/plot_normalization.html: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jeffsocal/tidyproteomics/HEAD/docs/reference/plot_normalization.html -------------------------------------------------------------------------------- /docs/reference/plot_pca-1.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jeffsocal/tidyproteomics/HEAD/docs/reference/plot_pca-1.png -------------------------------------------------------------------------------- /docs/reference/plot_pca-2.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jeffsocal/tidyproteomics/HEAD/docs/reference/plot_pca-2.png -------------------------------------------------------------------------------- /docs/reference/plot_pca-3.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jeffsocal/tidyproteomics/HEAD/docs/reference/plot_pca-3.png -------------------------------------------------------------------------------- /docs/reference/plot_pca.html: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jeffsocal/tidyproteomics/HEAD/docs/reference/plot_pca.html -------------------------------------------------------------------------------- /docs/reference/plot_proportion-1.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jeffsocal/tidyproteomics/HEAD/docs/reference/plot_proportion-1.png -------------------------------------------------------------------------------- /docs/reference/plot_proportion-2.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jeffsocal/tidyproteomics/HEAD/docs/reference/plot_proportion-2.png -------------------------------------------------------------------------------- /docs/reference/plot_proportion.html: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jeffsocal/tidyproteomics/HEAD/docs/reference/plot_proportion.html -------------------------------------------------------------------------------- /docs/reference/plot_protein-1.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jeffsocal/tidyproteomics/HEAD/docs/reference/plot_protein-1.png -------------------------------------------------------------------------------- /docs/reference/plot_protein.html: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jeffsocal/tidyproteomics/HEAD/docs/reference/plot_protein.html -------------------------------------------------------------------------------- /docs/reference/plot_quantrank-1.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jeffsocal/tidyproteomics/HEAD/docs/reference/plot_quantrank-1.png -------------------------------------------------------------------------------- /docs/reference/plot_quantrank-2.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jeffsocal/tidyproteomics/HEAD/docs/reference/plot_quantrank-2.png -------------------------------------------------------------------------------- /docs/reference/plot_quantrank-3.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jeffsocal/tidyproteomics/HEAD/docs/reference/plot_quantrank-3.png -------------------------------------------------------------------------------- /docs/reference/plot_quantrank-4.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jeffsocal/tidyproteomics/HEAD/docs/reference/plot_quantrank-4.png -------------------------------------------------------------------------------- /docs/reference/plot_quantrank.html: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jeffsocal/tidyproteomics/HEAD/docs/reference/plot_quantrank.html -------------------------------------------------------------------------------- /docs/reference/plot_save.html: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jeffsocal/tidyproteomics/HEAD/docs/reference/plot_save.html -------------------------------------------------------------------------------- /docs/reference/plot_variation_cv-1.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jeffsocal/tidyproteomics/HEAD/docs/reference/plot_variation_cv-1.png -------------------------------------------------------------------------------- /docs/reference/plot_variation_cv.html: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jeffsocal/tidyproteomics/HEAD/docs/reference/plot_variation_cv.html -------------------------------------------------------------------------------- /docs/reference/plot_variation_pca-1.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jeffsocal/tidyproteomics/HEAD/docs/reference/plot_variation_pca-1.png -------------------------------------------------------------------------------- /docs/reference/plot_variation_pca.html: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jeffsocal/tidyproteomics/HEAD/docs/reference/plot_variation_pca.html -------------------------------------------------------------------------------- /docs/reference/plot_venn-1.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jeffsocal/tidyproteomics/HEAD/docs/reference/plot_venn-1.png -------------------------------------------------------------------------------- /docs/reference/plot_venn.html: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jeffsocal/tidyproteomics/HEAD/docs/reference/plot_venn.html -------------------------------------------------------------------------------- /docs/reference/plot_volcano-1.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jeffsocal/tidyproteomics/HEAD/docs/reference/plot_volcano-1.png -------------------------------------------------------------------------------- /docs/reference/plot_volcano-2.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jeffsocal/tidyproteomics/HEAD/docs/reference/plot_volcano-2.png -------------------------------------------------------------------------------- /docs/reference/plot_volcano.html: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jeffsocal/tidyproteomics/HEAD/docs/reference/plot_volcano.html -------------------------------------------------------------------------------- /docs/reference/print.tidyproteomics.html: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jeffsocal/tidyproteomics/HEAD/docs/reference/print.tidyproteomics.html -------------------------------------------------------------------------------- /docs/reference/println.html: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jeffsocal/tidyproteomics/HEAD/docs/reference/println.html -------------------------------------------------------------------------------- /docs/reference/protein_map.html: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jeffsocal/tidyproteomics/HEAD/docs/reference/protein_map.html -------------------------------------------------------------------------------- /docs/reference/protein_map_munge.html: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jeffsocal/tidyproteomics/HEAD/docs/reference/protein_map_munge.html -------------------------------------------------------------------------------- /docs/reference/proteins_volcano_knockdown-control.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jeffsocal/tidyproteomics/HEAD/docs/reference/proteins_volcano_knockdown-control.png -------------------------------------------------------------------------------- /docs/reference/read_data.html: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jeffsocal/tidyproteomics/HEAD/docs/reference/read_data.html -------------------------------------------------------------------------------- /docs/reference/read_mzTab.html: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jeffsocal/tidyproteomics/HEAD/docs/reference/read_mzTab.html -------------------------------------------------------------------------------- /docs/reference/reassign.html: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jeffsocal/tidyproteomics/HEAD/docs/reference/reassign.html -------------------------------------------------------------------------------- /docs/reference/reverselog_transformation.html: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jeffsocal/tidyproteomics/HEAD/docs/reference/reverselog_transformation.html -------------------------------------------------------------------------------- /docs/reference/rf_parallel.html: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jeffsocal/tidyproteomics/HEAD/docs/reference/rf_parallel.html -------------------------------------------------------------------------------- /docs/reference/rm.mbr.html: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jeffsocal/tidyproteomics/HEAD/docs/reference/rm.mbr.html -------------------------------------------------------------------------------- /docs/reference/save_local.html: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jeffsocal/tidyproteomics/HEAD/docs/reference/save_local.html -------------------------------------------------------------------------------- /docs/reference/save_table.html: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jeffsocal/tidyproteomics/HEAD/docs/reference/save_table.html -------------------------------------------------------------------------------- /docs/reference/select_normalization.html: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jeffsocal/tidyproteomics/HEAD/docs/reference/select_normalization.html -------------------------------------------------------------------------------- /docs/reference/set_vect.html: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jeffsocal/tidyproteomics/HEAD/docs/reference/set_vect.html -------------------------------------------------------------------------------- /docs/reference/show_annotations.html: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jeffsocal/tidyproteomics/HEAD/docs/reference/show_annotations.html -------------------------------------------------------------------------------- /docs/reference/stats_contamination.html: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jeffsocal/tidyproteomics/HEAD/docs/reference/stats_contamination.html -------------------------------------------------------------------------------- /docs/reference/stats_print.html: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jeffsocal/tidyproteomics/HEAD/docs/reference/stats_print.html -------------------------------------------------------------------------------- /docs/reference/stats_summary.html: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jeffsocal/tidyproteomics/HEAD/docs/reference/stats_summary.html -------------------------------------------------------------------------------- /docs/reference/str_normalize.html: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jeffsocal/tidyproteomics/HEAD/docs/reference/str_normalize.html -------------------------------------------------------------------------------- /docs/reference/subset.html: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jeffsocal/tidyproteomics/HEAD/docs/reference/subset.html -------------------------------------------------------------------------------- /docs/reference/subset.tidyproteomics.html: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jeffsocal/tidyproteomics/HEAD/docs/reference/subset.tidyproteomics.html -------------------------------------------------------------------------------- /docs/reference/summary.tidyproteomics.html: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jeffsocal/tidyproteomics/HEAD/docs/reference/summary.tidyproteomics.html -------------------------------------------------------------------------------- /docs/reference/svm_parallel.html: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jeffsocal/tidyproteomics/HEAD/docs/reference/svm_parallel.html -------------------------------------------------------------------------------- /docs/reference/table_proteins_expression_knockdown-control.csv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jeffsocal/tidyproteomics/HEAD/docs/reference/table_proteins_expression_knockdown-control.csv -------------------------------------------------------------------------------- /docs/reference/table_quantrank-1.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jeffsocal/tidyproteomics/HEAD/docs/reference/table_quantrank-1.png -------------------------------------------------------------------------------- /docs/reference/table_quantrank-2.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jeffsocal/tidyproteomics/HEAD/docs/reference/table_quantrank-2.png -------------------------------------------------------------------------------- /docs/reference/table_quantrank-3.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jeffsocal/tidyproteomics/HEAD/docs/reference/table_quantrank-3.png -------------------------------------------------------------------------------- /docs/reference/table_quantrank.html: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jeffsocal/tidyproteomics/HEAD/docs/reference/table_quantrank.html -------------------------------------------------------------------------------- /docs/reference/theme_palette.html: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jeffsocal/tidyproteomics/HEAD/docs/reference/theme_palette.html -------------------------------------------------------------------------------- /docs/reference/tidyproteomics.html: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jeffsocal/tidyproteomics/HEAD/docs/reference/tidyproteomics.html -------------------------------------------------------------------------------- /docs/reference/tidyproteomics_quo.html: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jeffsocal/tidyproteomics/HEAD/docs/reference/tidyproteomics_quo.html -------------------------------------------------------------------------------- /docs/reference/tidyproteomics_quo_name.html: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jeffsocal/tidyproteomics/HEAD/docs/reference/tidyproteomics_quo_name.html -------------------------------------------------------------------------------- /docs/reference/tidyproteomics_summary.html: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jeffsocal/tidyproteomics/HEAD/docs/reference/tidyproteomics_summary.html -------------------------------------------------------------------------------- /docs/reference/transform_factor.html: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jeffsocal/tidyproteomics/HEAD/docs/reference/transform_factor.html -------------------------------------------------------------------------------- /docs/reference/transform_log2.html: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jeffsocal/tidyproteomics/HEAD/docs/reference/transform_log2.html -------------------------------------------------------------------------------- /docs/reference/transform_median.html: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jeffsocal/tidyproteomics/HEAD/docs/reference/transform_median.html -------------------------------------------------------------------------------- /docs/reference/write_local.html: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jeffsocal/tidyproteomics/HEAD/docs/reference/write_local.html -------------------------------------------------------------------------------- /docs/search.json: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jeffsocal/tidyproteomics/HEAD/docs/search.json -------------------------------------------------------------------------------- /docs/sitemap.xml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jeffsocal/tidyproteomics/HEAD/docs/sitemap.xml -------------------------------------------------------------------------------- /inst/extdata/config/DIA-NN_peptides.tsv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jeffsocal/tidyproteomics/HEAD/inst/extdata/config/DIA-NN_peptides.tsv -------------------------------------------------------------------------------- /inst/extdata/config/FragPipe_peptides.tsv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jeffsocal/tidyproteomics/HEAD/inst/extdata/config/FragPipe_peptides.tsv -------------------------------------------------------------------------------- /inst/extdata/config/FragPipe_proteins.tsv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jeffsocal/tidyproteomics/HEAD/inst/extdata/config/FragPipe_proteins.tsv -------------------------------------------------------------------------------- /inst/extdata/config/MaxQuant_peptides.tsv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jeffsocal/tidyproteomics/HEAD/inst/extdata/config/MaxQuant_peptides.tsv -------------------------------------------------------------------------------- /inst/extdata/config/MaxQuant_proteins.tsv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jeffsocal/tidyproteomics/HEAD/inst/extdata/config/MaxQuant_proteins.tsv -------------------------------------------------------------------------------- /inst/extdata/config/ProteomeDiscoverer_peptides.tsv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jeffsocal/tidyproteomics/HEAD/inst/extdata/config/ProteomeDiscoverer_peptides.tsv -------------------------------------------------------------------------------- /inst/extdata/config/ProteomeDiscoverer_proteins.tsv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jeffsocal/tidyproteomics/HEAD/inst/extdata/config/ProteomeDiscoverer_proteins.tsv -------------------------------------------------------------------------------- /inst/extdata/config/Skyline_peptides.tsv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jeffsocal/tidyproteomics/HEAD/inst/extdata/config/Skyline_peptides.tsv -------------------------------------------------------------------------------- /inst/extdata/config/mzTab_peptides.tsv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jeffsocal/tidyproteomics/HEAD/inst/extdata/config/mzTab_peptides.tsv -------------------------------------------------------------------------------- /inst/extdata/config/mzTab_proteins.tsv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jeffsocal/tidyproteomics/HEAD/inst/extdata/config/mzTab_proteins.tsv -------------------------------------------------------------------------------- /inst/extdata/human.fasta: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jeffsocal/tidyproteomics/HEAD/inst/extdata/human.fasta -------------------------------------------------------------------------------- /man/align_modification.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jeffsocal/tidyproteomics/HEAD/man/align_modification.Rd -------------------------------------------------------------------------------- /man/align_peptide.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jeffsocal/tidyproteomics/HEAD/man/align_peptide.Rd -------------------------------------------------------------------------------- /man/analysis_counts.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jeffsocal/tidyproteomics/HEAD/man/analysis_counts.Rd -------------------------------------------------------------------------------- /man/analyze_enrichments.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jeffsocal/tidyproteomics/HEAD/man/analyze_enrichments.Rd -------------------------------------------------------------------------------- /man/analyze_expressions.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jeffsocal/tidyproteomics/HEAD/man/analyze_expressions.Rd -------------------------------------------------------------------------------- /man/annotate.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jeffsocal/tidyproteomics/HEAD/man/annotate.Rd -------------------------------------------------------------------------------- /man/as.data.frame.tidyproteomics.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jeffsocal/tidyproteomics/HEAD/man/as.data.frame.tidyproteomics.Rd -------------------------------------------------------------------------------- /man/calc_enrichment.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jeffsocal/tidyproteomics/HEAD/man/calc_enrichment.Rd -------------------------------------------------------------------------------- /man/center.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jeffsocal/tidyproteomics/HEAD/man/center.Rd -------------------------------------------------------------------------------- /man/check_data.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jeffsocal/tidyproteomics/HEAD/man/check_data.Rd -------------------------------------------------------------------------------- /man/check_pairs.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jeffsocal/tidyproteomics/HEAD/man/check_pairs.Rd -------------------------------------------------------------------------------- /man/check_table.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jeffsocal/tidyproteomics/HEAD/man/check_table.Rd -------------------------------------------------------------------------------- /man/codify.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jeffsocal/tidyproteomics/HEAD/man/codify.Rd -------------------------------------------------------------------------------- /man/collapse.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jeffsocal/tidyproteomics/HEAD/man/collapse.Rd -------------------------------------------------------------------------------- /man/compute_compexp.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jeffsocal/tidyproteomics/HEAD/man/compute_compexp.Rd -------------------------------------------------------------------------------- /man/data_import.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jeffsocal/tidyproteomics/HEAD/man/data_import.Rd -------------------------------------------------------------------------------- /man/down_select.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jeffsocal/tidyproteomics/HEAD/man/down_select.Rd -------------------------------------------------------------------------------- /man/enrichment.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jeffsocal/tidyproteomics/HEAD/man/enrichment.Rd -------------------------------------------------------------------------------- /man/enrichment_fishersexact.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jeffsocal/tidyproteomics/HEAD/man/enrichment_fishersexact.Rd -------------------------------------------------------------------------------- /man/enrichment_gsea.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jeffsocal/tidyproteomics/HEAD/man/enrichment_gsea.Rd -------------------------------------------------------------------------------- /man/enrichment_wilcoxon.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jeffsocal/tidyproteomics/HEAD/man/enrichment_wilcoxon.Rd -------------------------------------------------------------------------------- /man/experimental.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jeffsocal/tidyproteomics/HEAD/man/experimental.Rd -------------------------------------------------------------------------------- /man/experimental_groups.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jeffsocal/tidyproteomics/HEAD/man/experimental_groups.Rd -------------------------------------------------------------------------------- /man/export_analysis.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jeffsocal/tidyproteomics/HEAD/man/export_analysis.Rd -------------------------------------------------------------------------------- /man/export_compexp.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jeffsocal/tidyproteomics/HEAD/man/export_compexp.Rd -------------------------------------------------------------------------------- /man/export_config.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jeffsocal/tidyproteomics/HEAD/man/export_config.Rd -------------------------------------------------------------------------------- /man/export_quant.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jeffsocal/tidyproteomics/HEAD/man/export_quant.Rd -------------------------------------------------------------------------------- /man/expression.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jeffsocal/tidyproteomics/HEAD/man/expression.Rd -------------------------------------------------------------------------------- /man/expression_limma.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jeffsocal/tidyproteomics/HEAD/man/expression_limma.Rd -------------------------------------------------------------------------------- /man/expression_test.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jeffsocal/tidyproteomics/HEAD/man/expression_test.Rd -------------------------------------------------------------------------------- /man/extract.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jeffsocal/tidyproteomics/HEAD/man/extract.Rd -------------------------------------------------------------------------------- /man/fasta_digest.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jeffsocal/tidyproteomics/HEAD/man/fasta_digest.Rd -------------------------------------------------------------------------------- /man/fasta_extract.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jeffsocal/tidyproteomics/HEAD/man/fasta_extract.Rd -------------------------------------------------------------------------------- /man/fasta_parse.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jeffsocal/tidyproteomics/HEAD/man/fasta_parse.Rd -------------------------------------------------------------------------------- /man/fasta_peptides.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jeffsocal/tidyproteomics/HEAD/man/fasta_peptides.Rd -------------------------------------------------------------------------------- /man/fasta_regex.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jeffsocal/tidyproteomics/HEAD/man/fasta_regex.Rd -------------------------------------------------------------------------------- /man/fgeomean.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jeffsocal/tidyproteomics/HEAD/man/fgeomean.Rd -------------------------------------------------------------------------------- /man/figures/logo.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jeffsocal/tidyproteomics/HEAD/man/figures/logo.png -------------------------------------------------------------------------------- /man/fmean.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jeffsocal/tidyproteomics/HEAD/man/fmean.Rd -------------------------------------------------------------------------------- /man/fmedian.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jeffsocal/tidyproteomics/HEAD/man/fmedian.Rd -------------------------------------------------------------------------------- /man/fmin.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jeffsocal/tidyproteomics/HEAD/man/fmin.Rd -------------------------------------------------------------------------------- /man/fsum.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jeffsocal/tidyproteomics/HEAD/man/fsum.Rd -------------------------------------------------------------------------------- /man/get_accountings.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jeffsocal/tidyproteomics/HEAD/man/get_accountings.Rd -------------------------------------------------------------------------------- /man/get_annotation_terms.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jeffsocal/tidyproteomics/HEAD/man/get_annotation_terms.Rd -------------------------------------------------------------------------------- /man/get_annotations.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jeffsocal/tidyproteomics/HEAD/man/get_annotations.Rd -------------------------------------------------------------------------------- /man/get_quant_names.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jeffsocal/tidyproteomics/HEAD/man/get_quant_names.Rd -------------------------------------------------------------------------------- /man/get_sample_names.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jeffsocal/tidyproteomics/HEAD/man/get_sample_names.Rd -------------------------------------------------------------------------------- /man/get_segment.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jeffsocal/tidyproteomics/HEAD/man/get_segment.Rd -------------------------------------------------------------------------------- /man/get_unique_variables.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jeffsocal/tidyproteomics/HEAD/man/get_unique_variables.Rd -------------------------------------------------------------------------------- /man/get_variables.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jeffsocal/tidyproteomics/HEAD/man/get_variables.Rd -------------------------------------------------------------------------------- /man/grapes-like-grapes.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jeffsocal/tidyproteomics/HEAD/man/grapes-like-grapes.Rd -------------------------------------------------------------------------------- /man/hash_vector.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jeffsocal/tidyproteomics/HEAD/man/hash_vector.Rd -------------------------------------------------------------------------------- /man/hdf.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jeffsocal/tidyproteomics/HEAD/man/hdf.Rd -------------------------------------------------------------------------------- /man/hela_peptides.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jeffsocal/tidyproteomics/HEAD/man/hela_peptides.Rd -------------------------------------------------------------------------------- /man/hela_proteins.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jeffsocal/tidyproteomics/HEAD/man/hela_proteins.Rd -------------------------------------------------------------------------------- /man/import.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jeffsocal/tidyproteomics/HEAD/man/import.Rd -------------------------------------------------------------------------------- /man/import_extract.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jeffsocal/tidyproteomics/HEAD/man/import_extract.Rd -------------------------------------------------------------------------------- /man/import_mbr.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jeffsocal/tidyproteomics/HEAD/man/import_mbr.Rd -------------------------------------------------------------------------------- /man/import_remove.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jeffsocal/tidyproteomics/HEAD/man/import_remove.Rd -------------------------------------------------------------------------------- /man/import_rename.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jeffsocal/tidyproteomics/HEAD/man/import_rename.Rd -------------------------------------------------------------------------------- /man/import_split.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jeffsocal/tidyproteomics/HEAD/man/import_split.Rd -------------------------------------------------------------------------------- /man/import_validate.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jeffsocal/tidyproteomics/HEAD/man/import_validate.Rd -------------------------------------------------------------------------------- /man/impute.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jeffsocal/tidyproteomics/HEAD/man/impute.Rd -------------------------------------------------------------------------------- /man/impute.randomforest.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jeffsocal/tidyproteomics/HEAD/man/impute.randomforest.Rd -------------------------------------------------------------------------------- /man/impute_ratio.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jeffsocal/tidyproteomics/HEAD/man/impute_ratio.Rd -------------------------------------------------------------------------------- /man/intersect_venn.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jeffsocal/tidyproteomics/HEAD/man/intersect_venn.Rd -------------------------------------------------------------------------------- /man/intersection.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jeffsocal/tidyproteomics/HEAD/man/intersection.Rd -------------------------------------------------------------------------------- /man/invlog2.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jeffsocal/tidyproteomics/HEAD/man/invlog2.Rd -------------------------------------------------------------------------------- /man/list_venn.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jeffsocal/tidyproteomics/HEAD/man/list_venn.Rd -------------------------------------------------------------------------------- /man/load_local.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jeffsocal/tidyproteomics/HEAD/man/load_local.Rd -------------------------------------------------------------------------------- /man/match_vect.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jeffsocal/tidyproteomics/HEAD/man/match_vect.Rd -------------------------------------------------------------------------------- /man/meld.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jeffsocal/tidyproteomics/HEAD/man/meld.Rd -------------------------------------------------------------------------------- /man/merge.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jeffsocal/tidyproteomics/HEAD/man/merge.Rd -------------------------------------------------------------------------------- /man/merge_quantitative.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jeffsocal/tidyproteomics/HEAD/man/merge_quantitative.Rd -------------------------------------------------------------------------------- /man/munge_identifier.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jeffsocal/tidyproteomics/HEAD/man/munge_identifier.Rd -------------------------------------------------------------------------------- /man/normalize.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jeffsocal/tidyproteomics/HEAD/man/normalize.Rd -------------------------------------------------------------------------------- /man/normalize_limma.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jeffsocal/tidyproteomics/HEAD/man/normalize_limma.Rd -------------------------------------------------------------------------------- /man/normalize_linear.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jeffsocal/tidyproteomics/HEAD/man/normalize_linear.Rd -------------------------------------------------------------------------------- /man/normalize_loess.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jeffsocal/tidyproteomics/HEAD/man/normalize_loess.Rd -------------------------------------------------------------------------------- /man/normalize_median.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jeffsocal/tidyproteomics/HEAD/man/normalize_median.Rd -------------------------------------------------------------------------------- /man/normalize_randomforest.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jeffsocal/tidyproteomics/HEAD/man/normalize_randomforest.Rd -------------------------------------------------------------------------------- /man/normalize_scaled.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jeffsocal/tidyproteomics/HEAD/man/normalize_scaled.Rd -------------------------------------------------------------------------------- /man/normalize_svm.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jeffsocal/tidyproteomics/HEAD/man/normalize_svm.Rd -------------------------------------------------------------------------------- /man/operations.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jeffsocal/tidyproteomics/HEAD/man/operations.Rd -------------------------------------------------------------------------------- /man/path_to_package_data.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jeffsocal/tidyproteomics/HEAD/man/path_to_package_data.Rd -------------------------------------------------------------------------------- /man/plot.tidyproteomics.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jeffsocal/tidyproteomics/HEAD/man/plot.tidyproteomics.Rd -------------------------------------------------------------------------------- /man/plot_compexp.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jeffsocal/tidyproteomics/HEAD/man/plot_compexp.Rd -------------------------------------------------------------------------------- /man/plot_counts.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jeffsocal/tidyproteomics/HEAD/man/plot_counts.Rd -------------------------------------------------------------------------------- /man/plot_dynamic_range.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jeffsocal/tidyproteomics/HEAD/man/plot_dynamic_range.Rd -------------------------------------------------------------------------------- /man/plot_enrichment.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jeffsocal/tidyproteomics/HEAD/man/plot_enrichment.Rd -------------------------------------------------------------------------------- /man/plot_euler.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jeffsocal/tidyproteomics/HEAD/man/plot_euler.Rd -------------------------------------------------------------------------------- /man/plot_heatmap.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jeffsocal/tidyproteomics/HEAD/man/plot_heatmap.Rd -------------------------------------------------------------------------------- /man/plot_normalization.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jeffsocal/tidyproteomics/HEAD/man/plot_normalization.Rd -------------------------------------------------------------------------------- /man/plot_pca.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jeffsocal/tidyproteomics/HEAD/man/plot_pca.Rd -------------------------------------------------------------------------------- /man/plot_proportion.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jeffsocal/tidyproteomics/HEAD/man/plot_proportion.Rd -------------------------------------------------------------------------------- /man/plot_protein.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jeffsocal/tidyproteomics/HEAD/man/plot_protein.Rd -------------------------------------------------------------------------------- /man/plot_quantrank.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jeffsocal/tidyproteomics/HEAD/man/plot_quantrank.Rd -------------------------------------------------------------------------------- /man/plot_save.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jeffsocal/tidyproteomics/HEAD/man/plot_save.Rd -------------------------------------------------------------------------------- /man/plot_variation_cv.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jeffsocal/tidyproteomics/HEAD/man/plot_variation_cv.Rd -------------------------------------------------------------------------------- /man/plot_variation_pca.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jeffsocal/tidyproteomics/HEAD/man/plot_variation_pca.Rd -------------------------------------------------------------------------------- /man/plot_venn.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jeffsocal/tidyproteomics/HEAD/man/plot_venn.Rd -------------------------------------------------------------------------------- /man/plot_volcano.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jeffsocal/tidyproteomics/HEAD/man/plot_volcano.Rd -------------------------------------------------------------------------------- /man/print.tidyproteomics.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jeffsocal/tidyproteomics/HEAD/man/print.tidyproteomics.Rd -------------------------------------------------------------------------------- /man/println.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jeffsocal/tidyproteomics/HEAD/man/println.Rd -------------------------------------------------------------------------------- /man/protein_map.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jeffsocal/tidyproteomics/HEAD/man/protein_map.Rd -------------------------------------------------------------------------------- /man/protein_map_munge.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jeffsocal/tidyproteomics/HEAD/man/protein_map_munge.Rd -------------------------------------------------------------------------------- /man/read_data.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jeffsocal/tidyproteomics/HEAD/man/read_data.Rd -------------------------------------------------------------------------------- /man/read_mzTab.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jeffsocal/tidyproteomics/HEAD/man/read_mzTab.Rd -------------------------------------------------------------------------------- /man/reassign.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jeffsocal/tidyproteomics/HEAD/man/reassign.Rd -------------------------------------------------------------------------------- /man/reverselog_transformation.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jeffsocal/tidyproteomics/HEAD/man/reverselog_transformation.Rd -------------------------------------------------------------------------------- /man/rf_parallel.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jeffsocal/tidyproteomics/HEAD/man/rf_parallel.Rd -------------------------------------------------------------------------------- /man/rm.mbr.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jeffsocal/tidyproteomics/HEAD/man/rm.mbr.Rd -------------------------------------------------------------------------------- /man/save_local.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jeffsocal/tidyproteomics/HEAD/man/save_local.Rd -------------------------------------------------------------------------------- /man/save_table.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jeffsocal/tidyproteomics/HEAD/man/save_table.Rd -------------------------------------------------------------------------------- /man/select_normalization.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jeffsocal/tidyproteomics/HEAD/man/select_normalization.Rd -------------------------------------------------------------------------------- /man/set_vect.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jeffsocal/tidyproteomics/HEAD/man/set_vect.Rd -------------------------------------------------------------------------------- /man/show_annotations.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jeffsocal/tidyproteomics/HEAD/man/show_annotations.Rd -------------------------------------------------------------------------------- /man/stats_contamination.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jeffsocal/tidyproteomics/HEAD/man/stats_contamination.Rd -------------------------------------------------------------------------------- /man/stats_print.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jeffsocal/tidyproteomics/HEAD/man/stats_print.Rd -------------------------------------------------------------------------------- /man/stats_summary.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jeffsocal/tidyproteomics/HEAD/man/stats_summary.Rd -------------------------------------------------------------------------------- /man/str_normalize.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jeffsocal/tidyproteomics/HEAD/man/str_normalize.Rd -------------------------------------------------------------------------------- /man/subset.tidyproteomics.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jeffsocal/tidyproteomics/HEAD/man/subset.tidyproteomics.Rd -------------------------------------------------------------------------------- /man/summary.tidyproteomics.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jeffsocal/tidyproteomics/HEAD/man/summary.tidyproteomics.Rd -------------------------------------------------------------------------------- /man/svm_parallel.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jeffsocal/tidyproteomics/HEAD/man/svm_parallel.Rd -------------------------------------------------------------------------------- /man/table_quantrank.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jeffsocal/tidyproteomics/HEAD/man/table_quantrank.Rd -------------------------------------------------------------------------------- /man/theme_palette.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jeffsocal/tidyproteomics/HEAD/man/theme_palette.Rd -------------------------------------------------------------------------------- /man/tidyproteomics.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jeffsocal/tidyproteomics/HEAD/man/tidyproteomics.Rd -------------------------------------------------------------------------------- /man/tidyproteomics_quo.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jeffsocal/tidyproteomics/HEAD/man/tidyproteomics_quo.Rd -------------------------------------------------------------------------------- /man/tidyproteomics_quo_name.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jeffsocal/tidyproteomics/HEAD/man/tidyproteomics_quo_name.Rd -------------------------------------------------------------------------------- /man/tidyproteomics_summary.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jeffsocal/tidyproteomics/HEAD/man/tidyproteomics_summary.Rd -------------------------------------------------------------------------------- /man/transform_factor.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jeffsocal/tidyproteomics/HEAD/man/transform_factor.Rd -------------------------------------------------------------------------------- /man/transform_log2.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jeffsocal/tidyproteomics/HEAD/man/transform_log2.Rd -------------------------------------------------------------------------------- /man/transform_median.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jeffsocal/tidyproteomics/HEAD/man/transform_median.Rd -------------------------------------------------------------------------------- /man/write_local.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jeffsocal/tidyproteomics/HEAD/man/write_local.Rd -------------------------------------------------------------------------------- /pkgdown/favicon/apple-touch-icon-120x120.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jeffsocal/tidyproteomics/HEAD/pkgdown/favicon/apple-touch-icon-120x120.png -------------------------------------------------------------------------------- /pkgdown/favicon/apple-touch-icon-152x152.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jeffsocal/tidyproteomics/HEAD/pkgdown/favicon/apple-touch-icon-152x152.png -------------------------------------------------------------------------------- /pkgdown/favicon/apple-touch-icon-180x180.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jeffsocal/tidyproteomics/HEAD/pkgdown/favicon/apple-touch-icon-180x180.png -------------------------------------------------------------------------------- /pkgdown/favicon/apple-touch-icon-60x60.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jeffsocal/tidyproteomics/HEAD/pkgdown/favicon/apple-touch-icon-60x60.png -------------------------------------------------------------------------------- /pkgdown/favicon/apple-touch-icon-76x76.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jeffsocal/tidyproteomics/HEAD/pkgdown/favicon/apple-touch-icon-76x76.png -------------------------------------------------------------------------------- /pkgdown/favicon/apple-touch-icon.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jeffsocal/tidyproteomics/HEAD/pkgdown/favicon/apple-touch-icon.png -------------------------------------------------------------------------------- /pkgdown/favicon/favicon-16x16.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jeffsocal/tidyproteomics/HEAD/pkgdown/favicon/favicon-16x16.png -------------------------------------------------------------------------------- /pkgdown/favicon/favicon-32x32.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jeffsocal/tidyproteomics/HEAD/pkgdown/favicon/favicon-32x32.png -------------------------------------------------------------------------------- /pkgdown/favicon/favicon.ico: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jeffsocal/tidyproteomics/HEAD/pkgdown/favicon/favicon.ico -------------------------------------------------------------------------------- /tests/test_import.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jeffsocal/tidyproteomics/HEAD/tests/test_import.R -------------------------------------------------------------------------------- /tests/testthat.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jeffsocal/tidyproteomics/HEAD/tests/testthat.R -------------------------------------------------------------------------------- /tests/testthat/test-fun_hdf.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jeffsocal/tidyproteomics/HEAD/tests/testthat/test-fun_hdf.R -------------------------------------------------------------------------------- /tests/testthat/test-fun_invlog2.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jeffsocal/tidyproteomics/HEAD/tests/testthat/test-fun_invlog2.R -------------------------------------------------------------------------------- /tests/testthat/test-fun_str_normalize.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jeffsocal/tidyproteomics/HEAD/tests/testthat/test-fun_str_normalize.R -------------------------------------------------------------------------------- /tidyproteomics.Rproj: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jeffsocal/tidyproteomics/HEAD/tidyproteomics.Rproj -------------------------------------------------------------------------------- /vignettes/annotating.Rmd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jeffsocal/tidyproteomics/HEAD/vignettes/annotating.Rmd -------------------------------------------------------------------------------- /vignettes/automating.Rmd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jeffsocal/tidyproteomics/HEAD/vignettes/automating.Rmd -------------------------------------------------------------------------------- /vignettes/collapsing.Rmd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jeffsocal/tidyproteomics/HEAD/vignettes/collapsing.Rmd -------------------------------------------------------------------------------- /vignettes/data-object.Rmd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jeffsocal/tidyproteomics/HEAD/vignettes/data-object.Rmd -------------------------------------------------------------------------------- /vignettes/enrichment.Rmd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jeffsocal/tidyproteomics/HEAD/vignettes/enrichment.Rmd -------------------------------------------------------------------------------- /vignettes/expression.Rmd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jeffsocal/tidyproteomics/HEAD/vignettes/expression.Rmd -------------------------------------------------------------------------------- /vignettes/extracting.Rmd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jeffsocal/tidyproteomics/HEAD/vignettes/extracting.Rmd -------------------------------------------------------------------------------- /vignettes/images/proteins_enrichment_knockdown-control.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jeffsocal/tidyproteomics/HEAD/vignettes/images/proteins_enrichment_knockdown-control.png -------------------------------------------------------------------------------- /vignettes/images/proteins_volcano_knockdown-control.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jeffsocal/tidyproteomics/HEAD/vignettes/images/proteins_volcano_knockdown-control.png -------------------------------------------------------------------------------- /vignettes/images/table_proteins_enrichment_knockdown-control.csv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jeffsocal/tidyproteomics/HEAD/vignettes/images/table_proteins_enrichment_knockdown-control.csv -------------------------------------------------------------------------------- /vignettes/images/table_proteins_expression_knockdown-control.csv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jeffsocal/tidyproteomics/HEAD/vignettes/images/table_proteins_expression_knockdown-control.csv -------------------------------------------------------------------------------- /vignettes/images/uniprot_search_01.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jeffsocal/tidyproteomics/HEAD/vignettes/images/uniprot_search_01.png -------------------------------------------------------------------------------- /vignettes/images/uniprot_search_02.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jeffsocal/tidyproteomics/HEAD/vignettes/images/uniprot_search_02.png -------------------------------------------------------------------------------- /vignettes/importing.Rmd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jeffsocal/tidyproteomics/HEAD/vignettes/importing.Rmd -------------------------------------------------------------------------------- /vignettes/imputing.Rmd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jeffsocal/tidyproteomics/HEAD/vignettes/imputing.Rmd -------------------------------------------------------------------------------- /vignettes/normalizing.Rmd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jeffsocal/tidyproteomics/HEAD/vignettes/normalizing.Rmd -------------------------------------------------------------------------------- /vignettes/overview.Rmd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jeffsocal/tidyproteomics/HEAD/vignettes/overview.Rmd -------------------------------------------------------------------------------- /vignettes/subsetting.Rmd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jeffsocal/tidyproteomics/HEAD/vignettes/subsetting.Rmd -------------------------------------------------------------------------------- /vignettes/summarizing.Rmd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jeffsocal/tidyproteomics/HEAD/vignettes/summarizing.Rmd -------------------------------------------------------------------------------- /vignettes/updates.Rmd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jeffsocal/tidyproteomics/HEAD/vignettes/updates.Rmd -------------------------------------------------------------------------------- /vignettes/visualizing.Rmd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jeffsocal/tidyproteomics/HEAD/vignettes/visualizing.Rmd -------------------------------------------------------------------------------- /vignettes/workflow-importing.Rmd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jeffsocal/tidyproteomics/HEAD/vignettes/workflow-importing.Rmd -------------------------------------------------------------------------------- /vignettes/workflow-publication.Rmd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jeffsocal/tidyproteomics/HEAD/vignettes/workflow-publication.Rmd -------------------------------------------------------------------------------- /vignettes/workflow-simple.Rmd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jeffsocal/tidyproteomics/HEAD/vignettes/workflow-simple.Rmd -------------------------------------------------------------------------------- /vignettes/workflow-userimport.Rmd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jeffsocal/tidyproteomics/HEAD/vignettes/workflow-userimport.Rmd --------------------------------------------------------------------------------