├── .gitignore ├── .tmp ├── ChromImpute_SRC ├── .gitignore ├── ChromImpute_coeffv.jar ├── ernst │ └── ChromImpute │ │ ├── ChromImpute.java │ │ ├── RegressionTree.java │ │ └── Util.java └── makefile ├── README.md ├── altindex_scripts ├── altindex_auxfunctions.R ├── altindex_build_list.R ├── altindex_mergepks.sh ├── auxfunc_masterlist.py ├── auxfunc_masterlist.pyc ├── plot_regulatory_elements_ML_intersection.ipynb ├── plot_statistics_ML_intersection.ipynb └── process_ML.py ├── auxiliary_chromImpute_functions.R ├── auxiliary_function_general_repel.R ├── auxiliary_gwastree_functions.R ├── auxiliary_gwastree_plotting_functions.R ├── auxiliary_parsimony_functions.R ├── cluster_scripts ├── check_ChromImpute.sh ├── run_ChromHMM.sh ├── run_ChromImpute.sh ├── run_Index_masterlist_gen.sh ├── run_calculate_mark_recovery_metrics.sh ├── run_calculate_mark_variability.sh ├── run_check_bw_outputs.sh ├── run_chmm_to_modules.sh ├── run_chmm_to_modules_innercmd.sh ├── run_distance_alltracks_v_alltracks.sh ├── run_distance_diff_obs_all.sh ├── run_distance_obs_all.sh ├── run_distance_on_difference_obsimp.sh ├── run_distance_on_obsimp.sh ├── run_distance_withinsample.sh ├── run_eval_signal_distribution.sh ├── run_get_proc_RNAseq.sh ├── run_liftOver_on_ChromHMM.sh ├── run_region_tracks_multires.sh ├── run_vplot.sh ├── submit_ChromImpute.sh ├── submit_aggregate_marks_chromhmm.sh ├── submit_chmm_to_modules.sh ├── submit_cluster_mat.sh ├── submit_create_chmm_statelist.sh ├── submit_distance_alltracks_v_alltracks.sh ├── submit_distance_difference_obsimp.sh ├── submit_distance_obs_all.sh ├── submit_distance_obsimp.sh ├── submit_enrichment_pipeline.sh ├── submit_extract_H3K27ac_on_DHS.sh ├── submit_get_process_RNAseq.sh ├── submit_modules_pipeline.sh └── submit_plot_impobs_groups.sh ├── config_ChromImpute.sh ├── editing_tools ├── collate_figures_latex.py └── tex_template_header.txt ├── eglinking ├── linking-xgboost.tar.gz ├── linking-xgboost │ ├── collate_linking_results.sh │ ├── condense_linking_results.sh │ ├── linking │ │ ├── chromhmm_state.py │ │ ├── feature.py │ │ ├── feature_own.py │ │ ├── gene_info.py │ │ ├── linking.py │ │ ├── linking_basic.py │ │ ├── linking_logistic.py │ │ ├── mark.py │ │ └── util.py │ ├── run_linking.sh │ ├── run_linking_dist.sh │ ├── run_linking_distonly.sh │ ├── run_linking_mark.sh │ └── submit_linking.sh ├── linking_0430 │ ├── data-gen │ │ └── get_enhancer_regions.py │ ├── linking-0430.zip │ ├── linking │ │ ├── chromhmm_state.py │ │ ├── extract.py │ │ ├── gene_info.py │ │ ├── linking.py │ │ └── util.py │ └── run_linking.sh ├── modified_linkingcode.tar.gz ├── old_eglinking │ ├── enhancer_gene_linking_v1_060819.ipynb │ ├── evaluate_predicted_links_file.R │ ├── make_test_links_dataframe.sh │ ├── test_calculate_correlation.R │ └── test_calculate_correlations.py ├── run.sh ├── run_classifier.sh ├── run_classifier_array.sh ├── setup_linking_data.sh └── src │ ├── bed.py │ ├── classifier.py │ ├── data.py │ ├── get_all_enhancer_regions.py │ ├── get_enhancer_regions.py │ ├── get_masterlist.py │ ├── get_tss.py │ ├── sample_grep.py │ ├── sample_mark_grep.py │ ├── sample_rna_grep.py │ └── save_mtx.py ├── encode_submission ├── chmm_bed_to_bed9.sh ├── encode_file_replacement.py ├── get_biosample_mapping.R ├── make_bw_metadata_table.R ├── make_chmm_metadata_table.R ├── run_encode_file_recompile_replace_bigwig.sh ├── run_encode_file_replace_bigwig.sh ├── run_encode_submission_bigwig.sh └── run_encode_submission_chromHMM.sh ├── epimapAUX ├── DESCRIPTION ├── NAMESPACE ├── R │ ├── enrichment_functions.R │ ├── epimap_specific_functions.R │ ├── general_repel_text.R │ ├── general_use_functions.R │ ├── matrix_functions.R │ └── text_processing_functions.R └── man │ ├── UpSet.v2.Rd │ ├── calc.breaks.Rd │ ├── calc.breaks.acut.Rd │ ├── calc.breaks.rect.Rd │ ├── capitalize.Rd │ ├── clamp.mat.Rd │ ├── corner.Rd │ ├── cosine.dist.Rd │ ├── diag.mat.Rd │ ├── diag.mat2.Rd │ ├── dot-ls.objects.Rd │ ├── general_repel_text.Rd │ ├── get_optimal_ordering.Rd │ ├── go.enr.Rd │ ├── jacc.dist.Rd │ ├── label.runs.Rd │ ├── logit.Rd │ ├── lsos.Rd │ ├── make.tform.Rd │ ├── meta.image.Rd │ ├── munge.nos.Rd │ ├── perc.rank.Rd │ ├── pivot.tomatrix.Rd │ ├── plot.cov.Rd │ ├── plot.dt.sym.Rd │ ├── process.dist.mat.Rd │ ├── reord.Rd │ ├── rsigm.Rd │ ├── run.fisher.Rd │ ├── run.hyper.Rd │ ├── set_proj.Rd │ ├── sigm.Rd │ ├── space.1d.Rd │ ├── split.text.Rd │ └── tsp.col.Rd ├── epimap_vis ├── auxiliary_plot_gwas.R ├── auxiliary_trackhubs_functions.R ├── data │ ├── 833_samples.txt │ ├── 859_samples.txt │ ├── all_assays.txt │ ├── all_enrichment_summaries_alone.Rda │ ├── all_gwas_SNP_links.Rda │ ├── all_released_tracks.tsv │ ├── all_snp_enrichment_labs_forfilt.Rda │ ├── all_snp_summaries_alone.Rda │ ├── all_snpxenhancer_intersections.Rda │ ├── centers_enrichmat_data.Rda │ ├── enhancer_tree_declist.Rda │ ├── group_ordering.tsv │ ├── gwascatalog_may03_2019_noquotes_summary.Rda │ ├── metadata_app.Rda │ ├── motif_modules_network_data.Rda │ ├── prelim_e4_bkpts_loc.tsv │ ├── tree_gwas1p_list.txt │ └── tree_gwas_list.txt ├── download.md ├── rsconnect │ └── shinyapps.io │ │ └── cboix │ │ └── epimap_vis.dcf ├── server.R ├── ui.R └── www │ └── jquery.elevatezoom.min.js ├── general_EPIMAP_ANALYSIS.R ├── great_enrichment ├── README.txt ├── auxfunctions_GREAT.R ├── code_coinertia.R ├── code_plot_GREAT_results.R ├── general_WM_functions.R ├── parse_GREAT_results.R ├── plot_GREAT_results.R ├── plot_GREAT_with_states_results.R ├── plot_great_alone.R ├── run_GREAT_submission.sh └── submit_GREAT_pipeline.sh ├── gwas_enrichment ├── ConvertPVALtoFDR.class ├── ConvertPVALtoFDR.java ├── MakeTableObservedFDR.class ├── MakeTableObservedFDR.java ├── StateMWGwasPeakHyper$Rec.class ├── StateMWGwasPeakHyper$RecBackFore.class ├── StateMWGwasPeakHyper$RecBackForeCompare.class ├── StateMWGwasPeakHyper$RecCompare.class ├── StateMWGwasPeakHyper.class ├── StateMWGwasPeakHyper.jar ├── StateMWGwasPeakHyper.java ├── StateMWGwasPeakHyperWithRandom.java ├── calculate_flat_hg_enr.R ├── calculate_flat_hg_enr_snpcentric.R ├── calculate_treebased_snpcentric.R ├── count_snps_tree.R ├── count_unique_enriched_snps.R ├── gwas_plotting │ ├── calculate_all_flat_enrichments.R │ ├── calculate_all_gwastree_enrichments.R │ ├── calculate_gwastree_consensus.R │ ├── calculate_gwastree_parsimony.R │ ├── create_gwas_intersect_matrix.sh │ ├── create_permuted_catalogs.R │ ├── create_shuffled_full_catalogs.R │ ├── eval_gwastree_strategies.R │ ├── eval_pvalue_cutoffs.R │ ├── eval_pvalue_cutoffs_FWER.R │ ├── explore_gwastree_methodology.R │ ├── extract_gwastree_snp_intersections.R │ ├── intersect_gwas_with_index.sh │ ├── plot_CAD_example_analysis.R │ ├── plot_CAD_sumstats_qqplots.R │ ├── plot_all_gwastree_example_analysis.R │ ├── plot_enrichments_gwastree.R │ ├── plot_explore_main_gwastree_examples.R │ ├── plot_gwas_flathg_alone.R │ ├── plot_gwas_flathg_alone.log │ ├── plot_gwas_hg_stats_from_tables.R │ ├── plot_gwas_tree.R │ ├── plot_gwas_with_ML.ipynb │ ├── plot_gwastree_construction_methods.R │ ├── plot_gwastree_example_figures.R │ ├── plot_gwastree_snp_intersections.R │ ├── plot_gwastree_snp_loci.R │ ├── plot_gwastree_snp_loci_mainfigures.R │ ├── plot_gwastree_tissue_breakpoints.R │ ├── plot_statistics_gwas_gwastree_enrichments.R │ ├── plot_statistics_tissue_gwastree_enrichments.R │ └── plot_statistics_validation_gwastree_enrichments.R ├── makefile ├── manifest.txt ├── munge_CAD_example_sumstats.sh ├── plot_flat_hg_enr.R ├── plot_gwas_alone.R ├── plot_gwastree_gwas_network.R ├── plot_gwastree_small_figures.R └── run_gwas_hg_pipeline.sh ├── ic_eval ├── aggregate_stats.sh ├── config_IC_files.sh ├── imputation_pick_subset.R ├── plot_rank_IC_metrics.R ├── process_IC_files.sh ├── run_IC_eval.sh └── run_IC_eval_pertrack.sh ├── imputation_analysis ├── calculate_bwtrack_similarity.py ├── calculate_diff_of_datasets.py ├── calculate_distance_of_datasets.py ├── calculate_enhancer_matrix_umap.py ├── calculate_inc_pca.py ├── calculate_mark_average_tracks.py ├── calculate_mark_recovery_metrics.py ├── calculate_mark_variability.py ├── calculate_markmatrix_variability.py ├── calculate_observed_emissions_overlap_chmm.R ├── calculate_permuted_flat_enrichments.R ├── calculate_permuted_gwastree_enrichments.R ├── calculate_prune_enhmat.R ├── calculate_unexpected_genes_modules.R ├── choose_rand_regions.R ├── collate_chromimpute_distance.sh ├── compile_plot_eval_metrics.sh ├── compute_IC_data_metrics.R ├── compute_coverage_overall_chromHMM.sh ├── convert_IC_data_hg19_fixedstep.sh ├── plot_IC_data_metrics.R ├── plot_IC_signal_distribution.R ├── plot_aggregate_stats_bwpk.R ├── plot_chromHMM_frequencies.R ├── plot_chromHMM_region.R ├── plot_chromImpute_diff_qc.R ├── plot_chromImpute_distance.R ├── plot_chromImpute_imputed_distance.R ├── plot_chromImpute_imputed_trees.R ├── plot_chromImpute_imputed_umap.R ├── plot_chromImpute_imputed_umap_homogeneity.R ├── plot_chromImpute_metrics.R ├── plot_chromImpute_metrics_bysupport.R ├── plot_chromImpute_metrics_final.R ├── plot_chromImpute_signal_distributions.R ├── plot_clusters_motifs.R ├── plot_datamatrix.R ├── plot_dataorigin.R ├── plot_datashader_matrix.py ├── plot_eval_diff_secondary.R ├── plot_eval_sampswaps.R ├── plot_example_impobs_nuc_regions.R ├── plot_impobs_groups.R ├── plot_impobs_tracks.R ├── plot_linked_enrichments_gwastree.R ├── plot_linking_02_corr_examples.R ├── plot_linking_03_localNMF_test.R ├── plot_linking_04_make_corr_fdr_pred.R ├── plot_linking_05_goenrichment.R ├── plot_linking_06_validation_figures.R ├── plot_modules_3panelsubsets.R ├── plot_modules_obsvalidation.R ├── plot_modules_only.R ├── plot_modules_with_fimo.R ├── plot_modules_with_great.R ├── plot_modules_with_gwas.R ├── plot_modules_with_gwas_flathg.R ├── plot_modules_with_motifs.R ├── plot_motifs_alone.R ├── plot_motifs_epigenomes_network.R ├── plot_observed_emissions_overlap_chmm.R ├── plot_own_masterlist_statistics.ipynb ├── plot_rand_regions.R ├── plot_reads_distribution.R ├── plot_sample_mark_chromImpute.R ├── plot_stats_bw_pk_intersection.R ├── plot_vplot.py ├── prioritize_diff_tracks.R ├── promoter_stats.R ├── query_motif_DHSlist.R ├── reduce_intersect_GTEx_eQTLs.sh └── uncertainty_analysis │ ├── compare_uncertainty_01_plot_tracks.R │ ├── compare_uncertainty_02_coeffv_vs_mark.R │ ├── compare_uncertainty_03_mark_matrices.R │ ├── compare_uncertainty_04_dnase_enhancer_intersect.R │ ├── compare_uncertainty_05_mark_recovery_metrics.R │ ├── compare_uncertainty_06_dhs_recovery_metrics.R │ └── compare_uncertainty_07_nondhs_recovery_metrics.R ├── impute_vis ├── data │ ├── DataSummary_ordered_distances.tsv │ ├── DataSummary_ordered_table.tsv │ ├── celltypes.tsv │ └── new_samples_mapping.tsv ├── imputation_avail_funcs.R ├── server.R └── ui.R ├── ldsc_enrichment ├── process_bed_to_annot.sh ├── process_gwas_dir_leadsnps.sh ├── process_gwas_dir_sumstats.sh ├── prune_leadsnps.py ├── run_partition_heritability_per_gwas.sh ├── submit_ldsc_pipeline.sh └── submit_process_gwas_dir_sumstats.sh ├── linking_methods └── Roadmap_Linking_YLiu.java ├── load_distance_matrices.R ├── load_gwastree_analysis.R ├── load_linking_data.py ├── load_linking_objects.R ├── load_metadata.R ├── load_modules_data.R ├── load_region_distance_matrices.R ├── load_statistics_gwastree_enrichments.R ├── load_updated_validation_enrichments.R ├── load_validation_gwastree_enrichments.R ├── main_EPIMAP_ANALYSIS.R ├── meme_enrichment ├── aggregate_parsed_fimo_results.R ├── aggregate_raw_fimo_results.R ├── parse_fimo_results.R ├── plot_fimo_alone.R ├── run_fimo.sh ├── run_fimo_db.sh └── submit_fimo_enrichment.sh ├── metadata_scripts ├── choose_expression_files.R ├── get_RNAseq_microarray_ENCODE.R ├── get_available_ENCODE_links.R ├── get_experiments_ENCODE.R ├── get_metadata_ENCODE.R ├── get_roadmap_mapping.R ├── imputation_avail_funcs.R ├── imputation_availability_table.R ├── make_trackhub_average_bigwigs.R ├── make_trackhub_bigwigs.R ├── make_trackhub_chromHMM.R └── make_trackhub_pergroup.R ├── motif_enrichment ├── compute_motif_enrichment.py ├── count_regions_bkg_motifs.py ├── motif_shuffle.py ├── plot_basic_motifs.R ├── plot_motif_logos.R ├── reduce_motif_matches.sh ├── run_motif_matches.sh ├── run_regions_bkg_comparison.sh ├── submit_motif_enrichment_pipe.sh └── submit_regions_bkg_comparison.sh ├── motifassoc_analysis └── calculate_motif_matrix.R ├── old_preprocessing_scripts ├── ATAC_pipeline.sh ├── BAMtoTA_download_preprocess.sh ├── Call_peaks.sh ├── ChIP_pipeline.sh ├── DNase_compute_window_occupancy.sh ├── DNase_download_preprocess.sh ├── Generate_signal_tracks.sh ├── Pool_subsample_SCCA.sh ├── by_header.awk ├── check_procfiles.sh ├── collate_expression_tsv.sh ├── determine_resampling_performance.sh ├── distance_between_binned.sh ├── distance_from_contingency.R ├── get_DNase_data.sh ├── get_IHEC_histone_bw_tracks.sh ├── get_roadmap_enh.sh ├── make_contingency_table_for_binned.sh ├── metrics_resampled_data.sh ├── plot_processing_status.R ├── plot_relevant_ChIPseq_expt.R ├── read_bw.cpp ├── run_ChIP_epitope.sh ├── run_ChIP_epitope_cell.sh ├── run_ChIP_parallel.sh ├── run_DNase_pipeline.sh ├── run_single_files.sh └── single_rep_peaks_signal.sh ├── postprocessing_scripts ├── convert_chmm_mat.sh ├── make_ChromHMM_bigbed_tracks.sh ├── make_and_transfer_bw_for_release.sh ├── make_average_bw_for_release.sh ├── make_bw_for_release.sh ├── merge_DHS_sites_public.R └── print_split_enh_out.R ├── preprocessing_pipeline ├── .gitignore ├── check_for_completion.sh ├── clean_empty_tagAligns.sh ├── clean_procfiles.sh ├── collate_CR_datasets.sh ├── collate_DHS_windows.sh ├── config.py ├── general.snake ├── generate_processing_status_report.sh ├── process_normalize_qc_RNAseq.R ├── project.snake ├── rules │ ├── BAMtoTA_download_preprocess.rules │ ├── call_peaks_macs.rules │ ├── compute_window_occupancy.rules │ ├── generate_signal_tracks_macs.rules │ └── pool_subsample_SCCA.rules ├── run_TF_epitopes.sh ├── run_minor_jobs.sh ├── run_snakemake.sh ├── submit_project_parallel.sh └── submit_snakemake_parallel.sh ├── screen_comparison ├── compare_to_screen_dels_01_overlap.R └── compare_to_screen_dels_02_gwas.R ├── setup_scripts ├── get_mappability_tracks.sh ├── install_processing_dependencies.sh ├── make_TSS_windows.sh ├── make_enhstate_list.sh ├── make_impobs_tables.sh └── make_uniform_control.sh ├── tree_vis ├── server.R └── ui.R └── utils ├── addRank2NarrowPeakFile.sh ├── aggregate_binary_txt_to_npy.py ├── bedgraph_compress.sh ├── callpeak_from_imputedbw.sh ├── catch_rerun.sh ├── chunk_bed.awk ├── clean_cpdir.sh ├── cluster_binary_mat.py ├── compress_bw_to_hd5py.py ├── convert_array_to_zarr.py ├── convert_meme_motifs.py ├── convert_to_fixed_step_bed.awk ├── create_chmm_state_possiblelist.py ├── extract_allbw_region.sh ├── extract_bw_bins.R ├── extract_bw_on_peaks.sh ├── extract_plot_chromHMM_region.sh ├── extract_signaldistr_statespecific.py ├── get_enh_prom_idx.py ├── merge_hdf5_matrices.py ├── parse_config.py ├── parse_config.pyc ├── precompute_correlations.py ├── proc_mtx_to_sparse.py └── txtdf_to_sparse.py /.gitignore: -------------------------------------------------------------------------------- 1 | .ipynb_checkpoints/ 2 | __pycache__/ 3 | *.parq/ 4 | -------------------------------------------------------------------------------- /.tmp: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cboix/EPIMAP_ANALYSIS/HEAD/.tmp -------------------------------------------------------------------------------- /ChromImpute_SRC/.gitignore: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cboix/EPIMAP_ANALYSIS/HEAD/ChromImpute_SRC/.gitignore -------------------------------------------------------------------------------- /ChromImpute_SRC/ChromImpute_coeffv.jar: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cboix/EPIMAP_ANALYSIS/HEAD/ChromImpute_SRC/ChromImpute_coeffv.jar -------------------------------------------------------------------------------- /ChromImpute_SRC/ernst/ChromImpute/ChromImpute.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cboix/EPIMAP_ANALYSIS/HEAD/ChromImpute_SRC/ernst/ChromImpute/ChromImpute.java -------------------------------------------------------------------------------- /ChromImpute_SRC/ernst/ChromImpute/RegressionTree.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cboix/EPIMAP_ANALYSIS/HEAD/ChromImpute_SRC/ernst/ChromImpute/RegressionTree.java -------------------------------------------------------------------------------- /ChromImpute_SRC/ernst/ChromImpute/Util.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cboix/EPIMAP_ANALYSIS/HEAD/ChromImpute_SRC/ernst/ChromImpute/Util.java -------------------------------------------------------------------------------- /ChromImpute_SRC/makefile: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cboix/EPIMAP_ANALYSIS/HEAD/ChromImpute_SRC/makefile -------------------------------------------------------------------------------- /README.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cboix/EPIMAP_ANALYSIS/HEAD/README.md -------------------------------------------------------------------------------- /altindex_scripts/altindex_auxfunctions.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cboix/EPIMAP_ANALYSIS/HEAD/altindex_scripts/altindex_auxfunctions.R -------------------------------------------------------------------------------- /altindex_scripts/altindex_build_list.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cboix/EPIMAP_ANALYSIS/HEAD/altindex_scripts/altindex_build_list.R -------------------------------------------------------------------------------- /altindex_scripts/altindex_mergepks.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cboix/EPIMAP_ANALYSIS/HEAD/altindex_scripts/altindex_mergepks.sh -------------------------------------------------------------------------------- /altindex_scripts/auxfunc_masterlist.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cboix/EPIMAP_ANALYSIS/HEAD/altindex_scripts/auxfunc_masterlist.py -------------------------------------------------------------------------------- /altindex_scripts/auxfunc_masterlist.pyc: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cboix/EPIMAP_ANALYSIS/HEAD/altindex_scripts/auxfunc_masterlist.pyc -------------------------------------------------------------------------------- /altindex_scripts/plot_regulatory_elements_ML_intersection.ipynb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cboix/EPIMAP_ANALYSIS/HEAD/altindex_scripts/plot_regulatory_elements_ML_intersection.ipynb -------------------------------------------------------------------------------- /altindex_scripts/plot_statistics_ML_intersection.ipynb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cboix/EPIMAP_ANALYSIS/HEAD/altindex_scripts/plot_statistics_ML_intersection.ipynb -------------------------------------------------------------------------------- /altindex_scripts/process_ML.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cboix/EPIMAP_ANALYSIS/HEAD/altindex_scripts/process_ML.py -------------------------------------------------------------------------------- /auxiliary_chromImpute_functions.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cboix/EPIMAP_ANALYSIS/HEAD/auxiliary_chromImpute_functions.R -------------------------------------------------------------------------------- /auxiliary_function_general_repel.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cboix/EPIMAP_ANALYSIS/HEAD/auxiliary_function_general_repel.R -------------------------------------------------------------------------------- /auxiliary_gwastree_functions.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cboix/EPIMAP_ANALYSIS/HEAD/auxiliary_gwastree_functions.R -------------------------------------------------------------------------------- /auxiliary_gwastree_plotting_functions.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cboix/EPIMAP_ANALYSIS/HEAD/auxiliary_gwastree_plotting_functions.R -------------------------------------------------------------------------------- /auxiliary_parsimony_functions.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cboix/EPIMAP_ANALYSIS/HEAD/auxiliary_parsimony_functions.R -------------------------------------------------------------------------------- /cluster_scripts/check_ChromImpute.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cboix/EPIMAP_ANALYSIS/HEAD/cluster_scripts/check_ChromImpute.sh -------------------------------------------------------------------------------- /cluster_scripts/run_ChromHMM.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cboix/EPIMAP_ANALYSIS/HEAD/cluster_scripts/run_ChromHMM.sh -------------------------------------------------------------------------------- /cluster_scripts/run_ChromImpute.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cboix/EPIMAP_ANALYSIS/HEAD/cluster_scripts/run_ChromImpute.sh -------------------------------------------------------------------------------- /cluster_scripts/run_Index_masterlist_gen.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cboix/EPIMAP_ANALYSIS/HEAD/cluster_scripts/run_Index_masterlist_gen.sh -------------------------------------------------------------------------------- /cluster_scripts/run_calculate_mark_recovery_metrics.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cboix/EPIMAP_ANALYSIS/HEAD/cluster_scripts/run_calculate_mark_recovery_metrics.sh -------------------------------------------------------------------------------- /cluster_scripts/run_calculate_mark_variability.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cboix/EPIMAP_ANALYSIS/HEAD/cluster_scripts/run_calculate_mark_variability.sh -------------------------------------------------------------------------------- /cluster_scripts/run_check_bw_outputs.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cboix/EPIMAP_ANALYSIS/HEAD/cluster_scripts/run_check_bw_outputs.sh -------------------------------------------------------------------------------- /cluster_scripts/run_chmm_to_modules.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cboix/EPIMAP_ANALYSIS/HEAD/cluster_scripts/run_chmm_to_modules.sh -------------------------------------------------------------------------------- /cluster_scripts/run_chmm_to_modules_innercmd.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cboix/EPIMAP_ANALYSIS/HEAD/cluster_scripts/run_chmm_to_modules_innercmd.sh -------------------------------------------------------------------------------- /cluster_scripts/run_distance_alltracks_v_alltracks.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cboix/EPIMAP_ANALYSIS/HEAD/cluster_scripts/run_distance_alltracks_v_alltracks.sh -------------------------------------------------------------------------------- /cluster_scripts/run_distance_diff_obs_all.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cboix/EPIMAP_ANALYSIS/HEAD/cluster_scripts/run_distance_diff_obs_all.sh -------------------------------------------------------------------------------- /cluster_scripts/run_distance_obs_all.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cboix/EPIMAP_ANALYSIS/HEAD/cluster_scripts/run_distance_obs_all.sh -------------------------------------------------------------------------------- /cluster_scripts/run_distance_on_difference_obsimp.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cboix/EPIMAP_ANALYSIS/HEAD/cluster_scripts/run_distance_on_difference_obsimp.sh -------------------------------------------------------------------------------- /cluster_scripts/run_distance_on_obsimp.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cboix/EPIMAP_ANALYSIS/HEAD/cluster_scripts/run_distance_on_obsimp.sh -------------------------------------------------------------------------------- /cluster_scripts/run_distance_withinsample.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cboix/EPIMAP_ANALYSIS/HEAD/cluster_scripts/run_distance_withinsample.sh -------------------------------------------------------------------------------- /cluster_scripts/run_eval_signal_distribution.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cboix/EPIMAP_ANALYSIS/HEAD/cluster_scripts/run_eval_signal_distribution.sh -------------------------------------------------------------------------------- /cluster_scripts/run_get_proc_RNAseq.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cboix/EPIMAP_ANALYSIS/HEAD/cluster_scripts/run_get_proc_RNAseq.sh -------------------------------------------------------------------------------- /cluster_scripts/run_liftOver_on_ChromHMM.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cboix/EPIMAP_ANALYSIS/HEAD/cluster_scripts/run_liftOver_on_ChromHMM.sh -------------------------------------------------------------------------------- /cluster_scripts/run_region_tracks_multires.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cboix/EPIMAP_ANALYSIS/HEAD/cluster_scripts/run_region_tracks_multires.sh -------------------------------------------------------------------------------- /cluster_scripts/run_vplot.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cboix/EPIMAP_ANALYSIS/HEAD/cluster_scripts/run_vplot.sh -------------------------------------------------------------------------------- /cluster_scripts/submit_ChromImpute.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cboix/EPIMAP_ANALYSIS/HEAD/cluster_scripts/submit_ChromImpute.sh -------------------------------------------------------------------------------- /cluster_scripts/submit_aggregate_marks_chromhmm.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cboix/EPIMAP_ANALYSIS/HEAD/cluster_scripts/submit_aggregate_marks_chromhmm.sh -------------------------------------------------------------------------------- /cluster_scripts/submit_chmm_to_modules.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cboix/EPIMAP_ANALYSIS/HEAD/cluster_scripts/submit_chmm_to_modules.sh -------------------------------------------------------------------------------- /cluster_scripts/submit_cluster_mat.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cboix/EPIMAP_ANALYSIS/HEAD/cluster_scripts/submit_cluster_mat.sh -------------------------------------------------------------------------------- /cluster_scripts/submit_create_chmm_statelist.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cboix/EPIMAP_ANALYSIS/HEAD/cluster_scripts/submit_create_chmm_statelist.sh -------------------------------------------------------------------------------- /cluster_scripts/submit_distance_alltracks_v_alltracks.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cboix/EPIMAP_ANALYSIS/HEAD/cluster_scripts/submit_distance_alltracks_v_alltracks.sh -------------------------------------------------------------------------------- /cluster_scripts/submit_distance_difference_obsimp.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cboix/EPIMAP_ANALYSIS/HEAD/cluster_scripts/submit_distance_difference_obsimp.sh -------------------------------------------------------------------------------- /cluster_scripts/submit_distance_obs_all.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cboix/EPIMAP_ANALYSIS/HEAD/cluster_scripts/submit_distance_obs_all.sh -------------------------------------------------------------------------------- /cluster_scripts/submit_distance_obsimp.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cboix/EPIMAP_ANALYSIS/HEAD/cluster_scripts/submit_distance_obsimp.sh -------------------------------------------------------------------------------- /cluster_scripts/submit_enrichment_pipeline.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cboix/EPIMAP_ANALYSIS/HEAD/cluster_scripts/submit_enrichment_pipeline.sh -------------------------------------------------------------------------------- /cluster_scripts/submit_extract_H3K27ac_on_DHS.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cboix/EPIMAP_ANALYSIS/HEAD/cluster_scripts/submit_extract_H3K27ac_on_DHS.sh -------------------------------------------------------------------------------- /cluster_scripts/submit_get_process_RNAseq.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cboix/EPIMAP_ANALYSIS/HEAD/cluster_scripts/submit_get_process_RNAseq.sh -------------------------------------------------------------------------------- /cluster_scripts/submit_modules_pipeline.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cboix/EPIMAP_ANALYSIS/HEAD/cluster_scripts/submit_modules_pipeline.sh -------------------------------------------------------------------------------- /cluster_scripts/submit_plot_impobs_groups.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cboix/EPIMAP_ANALYSIS/HEAD/cluster_scripts/submit_plot_impobs_groups.sh -------------------------------------------------------------------------------- /config_ChromImpute.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cboix/EPIMAP_ANALYSIS/HEAD/config_ChromImpute.sh -------------------------------------------------------------------------------- /editing_tools/collate_figures_latex.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cboix/EPIMAP_ANALYSIS/HEAD/editing_tools/collate_figures_latex.py -------------------------------------------------------------------------------- /editing_tools/tex_template_header.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cboix/EPIMAP_ANALYSIS/HEAD/editing_tools/tex_template_header.txt -------------------------------------------------------------------------------- /eglinking/linking-xgboost.tar.gz: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cboix/EPIMAP_ANALYSIS/HEAD/eglinking/linking-xgboost.tar.gz -------------------------------------------------------------------------------- /eglinking/linking-xgboost/collate_linking_results.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cboix/EPIMAP_ANALYSIS/HEAD/eglinking/linking-xgboost/collate_linking_results.sh -------------------------------------------------------------------------------- /eglinking/linking-xgboost/condense_linking_results.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cboix/EPIMAP_ANALYSIS/HEAD/eglinking/linking-xgboost/condense_linking_results.sh -------------------------------------------------------------------------------- /eglinking/linking-xgboost/linking/chromhmm_state.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cboix/EPIMAP_ANALYSIS/HEAD/eglinking/linking-xgboost/linking/chromhmm_state.py -------------------------------------------------------------------------------- /eglinking/linking-xgboost/linking/feature.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cboix/EPIMAP_ANALYSIS/HEAD/eglinking/linking-xgboost/linking/feature.py -------------------------------------------------------------------------------- /eglinking/linking-xgboost/linking/feature_own.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cboix/EPIMAP_ANALYSIS/HEAD/eglinking/linking-xgboost/linking/feature_own.py -------------------------------------------------------------------------------- /eglinking/linking-xgboost/linking/gene_info.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cboix/EPIMAP_ANALYSIS/HEAD/eglinking/linking-xgboost/linking/gene_info.py -------------------------------------------------------------------------------- /eglinking/linking-xgboost/linking/linking.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cboix/EPIMAP_ANALYSIS/HEAD/eglinking/linking-xgboost/linking/linking.py -------------------------------------------------------------------------------- /eglinking/linking-xgboost/linking/linking_basic.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cboix/EPIMAP_ANALYSIS/HEAD/eglinking/linking-xgboost/linking/linking_basic.py -------------------------------------------------------------------------------- /eglinking/linking-xgboost/linking/linking_logistic.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cboix/EPIMAP_ANALYSIS/HEAD/eglinking/linking-xgboost/linking/linking_logistic.py -------------------------------------------------------------------------------- /eglinking/linking-xgboost/linking/mark.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cboix/EPIMAP_ANALYSIS/HEAD/eglinking/linking-xgboost/linking/mark.py -------------------------------------------------------------------------------- /eglinking/linking-xgboost/linking/util.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cboix/EPIMAP_ANALYSIS/HEAD/eglinking/linking-xgboost/linking/util.py -------------------------------------------------------------------------------- /eglinking/linking-xgboost/run_linking.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cboix/EPIMAP_ANALYSIS/HEAD/eglinking/linking-xgboost/run_linking.sh -------------------------------------------------------------------------------- /eglinking/linking-xgboost/run_linking_dist.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cboix/EPIMAP_ANALYSIS/HEAD/eglinking/linking-xgboost/run_linking_dist.sh -------------------------------------------------------------------------------- /eglinking/linking-xgboost/run_linking_distonly.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cboix/EPIMAP_ANALYSIS/HEAD/eglinking/linking-xgboost/run_linking_distonly.sh -------------------------------------------------------------------------------- /eglinking/linking-xgboost/run_linking_mark.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cboix/EPIMAP_ANALYSIS/HEAD/eglinking/linking-xgboost/run_linking_mark.sh -------------------------------------------------------------------------------- /eglinking/linking-xgboost/submit_linking.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cboix/EPIMAP_ANALYSIS/HEAD/eglinking/linking-xgboost/submit_linking.sh -------------------------------------------------------------------------------- /eglinking/linking_0430/data-gen/get_enhancer_regions.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cboix/EPIMAP_ANALYSIS/HEAD/eglinking/linking_0430/data-gen/get_enhancer_regions.py -------------------------------------------------------------------------------- /eglinking/linking_0430/linking-0430.zip: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cboix/EPIMAP_ANALYSIS/HEAD/eglinking/linking_0430/linking-0430.zip -------------------------------------------------------------------------------- /eglinking/linking_0430/linking/chromhmm_state.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cboix/EPIMAP_ANALYSIS/HEAD/eglinking/linking_0430/linking/chromhmm_state.py -------------------------------------------------------------------------------- /eglinking/linking_0430/linking/extract.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cboix/EPIMAP_ANALYSIS/HEAD/eglinking/linking_0430/linking/extract.py -------------------------------------------------------------------------------- /eglinking/linking_0430/linking/gene_info.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cboix/EPIMAP_ANALYSIS/HEAD/eglinking/linking_0430/linking/gene_info.py -------------------------------------------------------------------------------- /eglinking/linking_0430/linking/linking.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cboix/EPIMAP_ANALYSIS/HEAD/eglinking/linking_0430/linking/linking.py -------------------------------------------------------------------------------- /eglinking/linking_0430/linking/util.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cboix/EPIMAP_ANALYSIS/HEAD/eglinking/linking_0430/linking/util.py -------------------------------------------------------------------------------- /eglinking/linking_0430/run_linking.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cboix/EPIMAP_ANALYSIS/HEAD/eglinking/linking_0430/run_linking.sh -------------------------------------------------------------------------------- /eglinking/modified_linkingcode.tar.gz: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cboix/EPIMAP_ANALYSIS/HEAD/eglinking/modified_linkingcode.tar.gz -------------------------------------------------------------------------------- /eglinking/old_eglinking/enhancer_gene_linking_v1_060819.ipynb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cboix/EPIMAP_ANALYSIS/HEAD/eglinking/old_eglinking/enhancer_gene_linking_v1_060819.ipynb -------------------------------------------------------------------------------- /eglinking/old_eglinking/evaluate_predicted_links_file.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cboix/EPIMAP_ANALYSIS/HEAD/eglinking/old_eglinking/evaluate_predicted_links_file.R -------------------------------------------------------------------------------- /eglinking/old_eglinking/make_test_links_dataframe.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cboix/EPIMAP_ANALYSIS/HEAD/eglinking/old_eglinking/make_test_links_dataframe.sh -------------------------------------------------------------------------------- /eglinking/old_eglinking/test_calculate_correlation.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cboix/EPIMAP_ANALYSIS/HEAD/eglinking/old_eglinking/test_calculate_correlation.R -------------------------------------------------------------------------------- /eglinking/old_eglinking/test_calculate_correlations.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cboix/EPIMAP_ANALYSIS/HEAD/eglinking/old_eglinking/test_calculate_correlations.py -------------------------------------------------------------------------------- /eglinking/run.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cboix/EPIMAP_ANALYSIS/HEAD/eglinking/run.sh -------------------------------------------------------------------------------- /eglinking/run_classifier.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cboix/EPIMAP_ANALYSIS/HEAD/eglinking/run_classifier.sh -------------------------------------------------------------------------------- /eglinking/run_classifier_array.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cboix/EPIMAP_ANALYSIS/HEAD/eglinking/run_classifier_array.sh -------------------------------------------------------------------------------- /eglinking/setup_linking_data.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cboix/EPIMAP_ANALYSIS/HEAD/eglinking/setup_linking_data.sh -------------------------------------------------------------------------------- /eglinking/src/bed.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cboix/EPIMAP_ANALYSIS/HEAD/eglinking/src/bed.py -------------------------------------------------------------------------------- /eglinking/src/classifier.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cboix/EPIMAP_ANALYSIS/HEAD/eglinking/src/classifier.py -------------------------------------------------------------------------------- /eglinking/src/data.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cboix/EPIMAP_ANALYSIS/HEAD/eglinking/src/data.py -------------------------------------------------------------------------------- /eglinking/src/get_all_enhancer_regions.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cboix/EPIMAP_ANALYSIS/HEAD/eglinking/src/get_all_enhancer_regions.py -------------------------------------------------------------------------------- /eglinking/src/get_enhancer_regions.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cboix/EPIMAP_ANALYSIS/HEAD/eglinking/src/get_enhancer_regions.py -------------------------------------------------------------------------------- /eglinking/src/get_masterlist.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cboix/EPIMAP_ANALYSIS/HEAD/eglinking/src/get_masterlist.py -------------------------------------------------------------------------------- /eglinking/src/get_tss.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cboix/EPIMAP_ANALYSIS/HEAD/eglinking/src/get_tss.py -------------------------------------------------------------------------------- /eglinking/src/sample_grep.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cboix/EPIMAP_ANALYSIS/HEAD/eglinking/src/sample_grep.py -------------------------------------------------------------------------------- /eglinking/src/sample_mark_grep.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cboix/EPIMAP_ANALYSIS/HEAD/eglinking/src/sample_mark_grep.py -------------------------------------------------------------------------------- /eglinking/src/sample_rna_grep.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cboix/EPIMAP_ANALYSIS/HEAD/eglinking/src/sample_rna_grep.py -------------------------------------------------------------------------------- /eglinking/src/save_mtx.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cboix/EPIMAP_ANALYSIS/HEAD/eglinking/src/save_mtx.py -------------------------------------------------------------------------------- /encode_submission/chmm_bed_to_bed9.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cboix/EPIMAP_ANALYSIS/HEAD/encode_submission/chmm_bed_to_bed9.sh -------------------------------------------------------------------------------- /encode_submission/encode_file_replacement.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cboix/EPIMAP_ANALYSIS/HEAD/encode_submission/encode_file_replacement.py -------------------------------------------------------------------------------- /encode_submission/get_biosample_mapping.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cboix/EPIMAP_ANALYSIS/HEAD/encode_submission/get_biosample_mapping.R -------------------------------------------------------------------------------- /encode_submission/make_bw_metadata_table.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cboix/EPIMAP_ANALYSIS/HEAD/encode_submission/make_bw_metadata_table.R -------------------------------------------------------------------------------- /encode_submission/make_chmm_metadata_table.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cboix/EPIMAP_ANALYSIS/HEAD/encode_submission/make_chmm_metadata_table.R -------------------------------------------------------------------------------- /encode_submission/run_encode_file_recompile_replace_bigwig.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cboix/EPIMAP_ANALYSIS/HEAD/encode_submission/run_encode_file_recompile_replace_bigwig.sh -------------------------------------------------------------------------------- /encode_submission/run_encode_file_replace_bigwig.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cboix/EPIMAP_ANALYSIS/HEAD/encode_submission/run_encode_file_replace_bigwig.sh -------------------------------------------------------------------------------- /encode_submission/run_encode_submission_bigwig.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cboix/EPIMAP_ANALYSIS/HEAD/encode_submission/run_encode_submission_bigwig.sh -------------------------------------------------------------------------------- /encode_submission/run_encode_submission_chromHMM.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cboix/EPIMAP_ANALYSIS/HEAD/encode_submission/run_encode_submission_chromHMM.sh -------------------------------------------------------------------------------- /epimapAUX/DESCRIPTION: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cboix/EPIMAP_ANALYSIS/HEAD/epimapAUX/DESCRIPTION -------------------------------------------------------------------------------- /epimapAUX/NAMESPACE: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cboix/EPIMAP_ANALYSIS/HEAD/epimapAUX/NAMESPACE -------------------------------------------------------------------------------- /epimapAUX/R/enrichment_functions.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cboix/EPIMAP_ANALYSIS/HEAD/epimapAUX/R/enrichment_functions.R -------------------------------------------------------------------------------- /epimapAUX/R/epimap_specific_functions.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cboix/EPIMAP_ANALYSIS/HEAD/epimapAUX/R/epimap_specific_functions.R -------------------------------------------------------------------------------- /epimapAUX/R/general_repel_text.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cboix/EPIMAP_ANALYSIS/HEAD/epimapAUX/R/general_repel_text.R -------------------------------------------------------------------------------- /epimapAUX/R/general_use_functions.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cboix/EPIMAP_ANALYSIS/HEAD/epimapAUX/R/general_use_functions.R -------------------------------------------------------------------------------- /epimapAUX/R/matrix_functions.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cboix/EPIMAP_ANALYSIS/HEAD/epimapAUX/R/matrix_functions.R -------------------------------------------------------------------------------- /epimapAUX/R/text_processing_functions.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cboix/EPIMAP_ANALYSIS/HEAD/epimapAUX/R/text_processing_functions.R -------------------------------------------------------------------------------- /epimapAUX/man/UpSet.v2.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cboix/EPIMAP_ANALYSIS/HEAD/epimapAUX/man/UpSet.v2.Rd -------------------------------------------------------------------------------- /epimapAUX/man/calc.breaks.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cboix/EPIMAP_ANALYSIS/HEAD/epimapAUX/man/calc.breaks.Rd -------------------------------------------------------------------------------- /epimapAUX/man/calc.breaks.acut.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cboix/EPIMAP_ANALYSIS/HEAD/epimapAUX/man/calc.breaks.acut.Rd -------------------------------------------------------------------------------- /epimapAUX/man/calc.breaks.rect.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cboix/EPIMAP_ANALYSIS/HEAD/epimapAUX/man/calc.breaks.rect.Rd -------------------------------------------------------------------------------- /epimapAUX/man/capitalize.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cboix/EPIMAP_ANALYSIS/HEAD/epimapAUX/man/capitalize.Rd -------------------------------------------------------------------------------- /epimapAUX/man/clamp.mat.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cboix/EPIMAP_ANALYSIS/HEAD/epimapAUX/man/clamp.mat.Rd -------------------------------------------------------------------------------- /epimapAUX/man/corner.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cboix/EPIMAP_ANALYSIS/HEAD/epimapAUX/man/corner.Rd -------------------------------------------------------------------------------- /epimapAUX/man/cosine.dist.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cboix/EPIMAP_ANALYSIS/HEAD/epimapAUX/man/cosine.dist.Rd -------------------------------------------------------------------------------- /epimapAUX/man/diag.mat.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cboix/EPIMAP_ANALYSIS/HEAD/epimapAUX/man/diag.mat.Rd -------------------------------------------------------------------------------- /epimapAUX/man/diag.mat2.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cboix/EPIMAP_ANALYSIS/HEAD/epimapAUX/man/diag.mat2.Rd -------------------------------------------------------------------------------- /epimapAUX/man/dot-ls.objects.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cboix/EPIMAP_ANALYSIS/HEAD/epimapAUX/man/dot-ls.objects.Rd -------------------------------------------------------------------------------- /epimapAUX/man/general_repel_text.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cboix/EPIMAP_ANALYSIS/HEAD/epimapAUX/man/general_repel_text.Rd -------------------------------------------------------------------------------- /epimapAUX/man/get_optimal_ordering.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cboix/EPIMAP_ANALYSIS/HEAD/epimapAUX/man/get_optimal_ordering.Rd -------------------------------------------------------------------------------- /epimapAUX/man/go.enr.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cboix/EPIMAP_ANALYSIS/HEAD/epimapAUX/man/go.enr.Rd -------------------------------------------------------------------------------- /epimapAUX/man/jacc.dist.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cboix/EPIMAP_ANALYSIS/HEAD/epimapAUX/man/jacc.dist.Rd -------------------------------------------------------------------------------- /epimapAUX/man/label.runs.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cboix/EPIMAP_ANALYSIS/HEAD/epimapAUX/man/label.runs.Rd -------------------------------------------------------------------------------- /epimapAUX/man/logit.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cboix/EPIMAP_ANALYSIS/HEAD/epimapAUX/man/logit.Rd -------------------------------------------------------------------------------- /epimapAUX/man/lsos.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cboix/EPIMAP_ANALYSIS/HEAD/epimapAUX/man/lsos.Rd -------------------------------------------------------------------------------- /epimapAUX/man/make.tform.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cboix/EPIMAP_ANALYSIS/HEAD/epimapAUX/man/make.tform.Rd -------------------------------------------------------------------------------- /epimapAUX/man/meta.image.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cboix/EPIMAP_ANALYSIS/HEAD/epimapAUX/man/meta.image.Rd -------------------------------------------------------------------------------- /epimapAUX/man/munge.nos.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cboix/EPIMAP_ANALYSIS/HEAD/epimapAUX/man/munge.nos.Rd -------------------------------------------------------------------------------- /epimapAUX/man/perc.rank.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cboix/EPIMAP_ANALYSIS/HEAD/epimapAUX/man/perc.rank.Rd -------------------------------------------------------------------------------- /epimapAUX/man/pivot.tomatrix.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cboix/EPIMAP_ANALYSIS/HEAD/epimapAUX/man/pivot.tomatrix.Rd -------------------------------------------------------------------------------- /epimapAUX/man/plot.cov.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cboix/EPIMAP_ANALYSIS/HEAD/epimapAUX/man/plot.cov.Rd -------------------------------------------------------------------------------- /epimapAUX/man/plot.dt.sym.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cboix/EPIMAP_ANALYSIS/HEAD/epimapAUX/man/plot.dt.sym.Rd -------------------------------------------------------------------------------- /epimapAUX/man/process.dist.mat.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cboix/EPIMAP_ANALYSIS/HEAD/epimapAUX/man/process.dist.mat.Rd -------------------------------------------------------------------------------- /epimapAUX/man/reord.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cboix/EPIMAP_ANALYSIS/HEAD/epimapAUX/man/reord.Rd -------------------------------------------------------------------------------- /epimapAUX/man/rsigm.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cboix/EPIMAP_ANALYSIS/HEAD/epimapAUX/man/rsigm.Rd -------------------------------------------------------------------------------- /epimapAUX/man/run.fisher.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cboix/EPIMAP_ANALYSIS/HEAD/epimapAUX/man/run.fisher.Rd -------------------------------------------------------------------------------- /epimapAUX/man/run.hyper.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cboix/EPIMAP_ANALYSIS/HEAD/epimapAUX/man/run.hyper.Rd -------------------------------------------------------------------------------- /epimapAUX/man/set_proj.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cboix/EPIMAP_ANALYSIS/HEAD/epimapAUX/man/set_proj.Rd -------------------------------------------------------------------------------- /epimapAUX/man/sigm.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cboix/EPIMAP_ANALYSIS/HEAD/epimapAUX/man/sigm.Rd -------------------------------------------------------------------------------- /epimapAUX/man/space.1d.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cboix/EPIMAP_ANALYSIS/HEAD/epimapAUX/man/space.1d.Rd -------------------------------------------------------------------------------- /epimapAUX/man/split.text.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cboix/EPIMAP_ANALYSIS/HEAD/epimapAUX/man/split.text.Rd -------------------------------------------------------------------------------- /epimapAUX/man/tsp.col.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cboix/EPIMAP_ANALYSIS/HEAD/epimapAUX/man/tsp.col.Rd -------------------------------------------------------------------------------- /epimap_vis/auxiliary_plot_gwas.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cboix/EPIMAP_ANALYSIS/HEAD/epimap_vis/auxiliary_plot_gwas.R -------------------------------------------------------------------------------- /epimap_vis/auxiliary_trackhubs_functions.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cboix/EPIMAP_ANALYSIS/HEAD/epimap_vis/auxiliary_trackhubs_functions.R -------------------------------------------------------------------------------- /epimap_vis/data/833_samples.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cboix/EPIMAP_ANALYSIS/HEAD/epimap_vis/data/833_samples.txt -------------------------------------------------------------------------------- /epimap_vis/data/859_samples.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cboix/EPIMAP_ANALYSIS/HEAD/epimap_vis/data/859_samples.txt -------------------------------------------------------------------------------- /epimap_vis/data/all_assays.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cboix/EPIMAP_ANALYSIS/HEAD/epimap_vis/data/all_assays.txt -------------------------------------------------------------------------------- /epimap_vis/data/all_enrichment_summaries_alone.Rda: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cboix/EPIMAP_ANALYSIS/HEAD/epimap_vis/data/all_enrichment_summaries_alone.Rda -------------------------------------------------------------------------------- /epimap_vis/data/all_gwas_SNP_links.Rda: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cboix/EPIMAP_ANALYSIS/HEAD/epimap_vis/data/all_gwas_SNP_links.Rda -------------------------------------------------------------------------------- /epimap_vis/data/all_released_tracks.tsv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cboix/EPIMAP_ANALYSIS/HEAD/epimap_vis/data/all_released_tracks.tsv -------------------------------------------------------------------------------- /epimap_vis/data/all_snp_enrichment_labs_forfilt.Rda: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cboix/EPIMAP_ANALYSIS/HEAD/epimap_vis/data/all_snp_enrichment_labs_forfilt.Rda -------------------------------------------------------------------------------- /epimap_vis/data/all_snp_summaries_alone.Rda: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cboix/EPIMAP_ANALYSIS/HEAD/epimap_vis/data/all_snp_summaries_alone.Rda -------------------------------------------------------------------------------- /epimap_vis/data/all_snpxenhancer_intersections.Rda: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cboix/EPIMAP_ANALYSIS/HEAD/epimap_vis/data/all_snpxenhancer_intersections.Rda -------------------------------------------------------------------------------- /epimap_vis/data/centers_enrichmat_data.Rda: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cboix/EPIMAP_ANALYSIS/HEAD/epimap_vis/data/centers_enrichmat_data.Rda -------------------------------------------------------------------------------- /epimap_vis/data/enhancer_tree_declist.Rda: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cboix/EPIMAP_ANALYSIS/HEAD/epimap_vis/data/enhancer_tree_declist.Rda -------------------------------------------------------------------------------- /epimap_vis/data/group_ordering.tsv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cboix/EPIMAP_ANALYSIS/HEAD/epimap_vis/data/group_ordering.tsv -------------------------------------------------------------------------------- /epimap_vis/data/gwascatalog_may03_2019_noquotes_summary.Rda: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cboix/EPIMAP_ANALYSIS/HEAD/epimap_vis/data/gwascatalog_may03_2019_noquotes_summary.Rda -------------------------------------------------------------------------------- /epimap_vis/data/metadata_app.Rda: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cboix/EPIMAP_ANALYSIS/HEAD/epimap_vis/data/metadata_app.Rda -------------------------------------------------------------------------------- /epimap_vis/data/motif_modules_network_data.Rda: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cboix/EPIMAP_ANALYSIS/HEAD/epimap_vis/data/motif_modules_network_data.Rda -------------------------------------------------------------------------------- /epimap_vis/data/prelim_e4_bkpts_loc.tsv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cboix/EPIMAP_ANALYSIS/HEAD/epimap_vis/data/prelim_e4_bkpts_loc.tsv -------------------------------------------------------------------------------- /epimap_vis/data/tree_gwas1p_list.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cboix/EPIMAP_ANALYSIS/HEAD/epimap_vis/data/tree_gwas1p_list.txt -------------------------------------------------------------------------------- /epimap_vis/data/tree_gwas_list.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cboix/EPIMAP_ANALYSIS/HEAD/epimap_vis/data/tree_gwas_list.txt -------------------------------------------------------------------------------- /epimap_vis/download.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cboix/EPIMAP_ANALYSIS/HEAD/epimap_vis/download.md -------------------------------------------------------------------------------- /epimap_vis/rsconnect/shinyapps.io/cboix/epimap_vis.dcf: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cboix/EPIMAP_ANALYSIS/HEAD/epimap_vis/rsconnect/shinyapps.io/cboix/epimap_vis.dcf -------------------------------------------------------------------------------- /epimap_vis/server.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cboix/EPIMAP_ANALYSIS/HEAD/epimap_vis/server.R -------------------------------------------------------------------------------- /epimap_vis/ui.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cboix/EPIMAP_ANALYSIS/HEAD/epimap_vis/ui.R -------------------------------------------------------------------------------- /epimap_vis/www/jquery.elevatezoom.min.js: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cboix/EPIMAP_ANALYSIS/HEAD/epimap_vis/www/jquery.elevatezoom.min.js -------------------------------------------------------------------------------- /general_EPIMAP_ANALYSIS.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cboix/EPIMAP_ANALYSIS/HEAD/general_EPIMAP_ANALYSIS.R -------------------------------------------------------------------------------- /great_enrichment/README.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cboix/EPIMAP_ANALYSIS/HEAD/great_enrichment/README.txt -------------------------------------------------------------------------------- /great_enrichment/auxfunctions_GREAT.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cboix/EPIMAP_ANALYSIS/HEAD/great_enrichment/auxfunctions_GREAT.R -------------------------------------------------------------------------------- /great_enrichment/code_coinertia.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cboix/EPIMAP_ANALYSIS/HEAD/great_enrichment/code_coinertia.R -------------------------------------------------------------------------------- /great_enrichment/code_plot_GREAT_results.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cboix/EPIMAP_ANALYSIS/HEAD/great_enrichment/code_plot_GREAT_results.R -------------------------------------------------------------------------------- /great_enrichment/general_WM_functions.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cboix/EPIMAP_ANALYSIS/HEAD/great_enrichment/general_WM_functions.R -------------------------------------------------------------------------------- /great_enrichment/parse_GREAT_results.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cboix/EPIMAP_ANALYSIS/HEAD/great_enrichment/parse_GREAT_results.R -------------------------------------------------------------------------------- /great_enrichment/plot_GREAT_results.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cboix/EPIMAP_ANALYSIS/HEAD/great_enrichment/plot_GREAT_results.R -------------------------------------------------------------------------------- /great_enrichment/plot_GREAT_with_states_results.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cboix/EPIMAP_ANALYSIS/HEAD/great_enrichment/plot_GREAT_with_states_results.R -------------------------------------------------------------------------------- /great_enrichment/plot_great_alone.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cboix/EPIMAP_ANALYSIS/HEAD/great_enrichment/plot_great_alone.R -------------------------------------------------------------------------------- /great_enrichment/run_GREAT_submission.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cboix/EPIMAP_ANALYSIS/HEAD/great_enrichment/run_GREAT_submission.sh -------------------------------------------------------------------------------- /great_enrichment/submit_GREAT_pipeline.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cboix/EPIMAP_ANALYSIS/HEAD/great_enrichment/submit_GREAT_pipeline.sh -------------------------------------------------------------------------------- /gwas_enrichment/ConvertPVALtoFDR.class: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cboix/EPIMAP_ANALYSIS/HEAD/gwas_enrichment/ConvertPVALtoFDR.class -------------------------------------------------------------------------------- /gwas_enrichment/ConvertPVALtoFDR.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cboix/EPIMAP_ANALYSIS/HEAD/gwas_enrichment/ConvertPVALtoFDR.java -------------------------------------------------------------------------------- /gwas_enrichment/MakeTableObservedFDR.class: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cboix/EPIMAP_ANALYSIS/HEAD/gwas_enrichment/MakeTableObservedFDR.class -------------------------------------------------------------------------------- /gwas_enrichment/MakeTableObservedFDR.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cboix/EPIMAP_ANALYSIS/HEAD/gwas_enrichment/MakeTableObservedFDR.java -------------------------------------------------------------------------------- /gwas_enrichment/StateMWGwasPeakHyper$Rec.class: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cboix/EPIMAP_ANALYSIS/HEAD/gwas_enrichment/StateMWGwasPeakHyper$Rec.class -------------------------------------------------------------------------------- /gwas_enrichment/StateMWGwasPeakHyper$RecBackFore.class: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cboix/EPIMAP_ANALYSIS/HEAD/gwas_enrichment/StateMWGwasPeakHyper$RecBackFore.class -------------------------------------------------------------------------------- /gwas_enrichment/StateMWGwasPeakHyper$RecBackForeCompare.class: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cboix/EPIMAP_ANALYSIS/HEAD/gwas_enrichment/StateMWGwasPeakHyper$RecBackForeCompare.class -------------------------------------------------------------------------------- /gwas_enrichment/StateMWGwasPeakHyper$RecCompare.class: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cboix/EPIMAP_ANALYSIS/HEAD/gwas_enrichment/StateMWGwasPeakHyper$RecCompare.class -------------------------------------------------------------------------------- /gwas_enrichment/StateMWGwasPeakHyper.class: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cboix/EPIMAP_ANALYSIS/HEAD/gwas_enrichment/StateMWGwasPeakHyper.class -------------------------------------------------------------------------------- /gwas_enrichment/StateMWGwasPeakHyper.jar: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cboix/EPIMAP_ANALYSIS/HEAD/gwas_enrichment/StateMWGwasPeakHyper.jar -------------------------------------------------------------------------------- /gwas_enrichment/StateMWGwasPeakHyper.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cboix/EPIMAP_ANALYSIS/HEAD/gwas_enrichment/StateMWGwasPeakHyper.java -------------------------------------------------------------------------------- /gwas_enrichment/StateMWGwasPeakHyperWithRandom.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cboix/EPIMAP_ANALYSIS/HEAD/gwas_enrichment/StateMWGwasPeakHyperWithRandom.java -------------------------------------------------------------------------------- /gwas_enrichment/calculate_flat_hg_enr.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cboix/EPIMAP_ANALYSIS/HEAD/gwas_enrichment/calculate_flat_hg_enr.R -------------------------------------------------------------------------------- /gwas_enrichment/calculate_flat_hg_enr_snpcentric.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cboix/EPIMAP_ANALYSIS/HEAD/gwas_enrichment/calculate_flat_hg_enr_snpcentric.R -------------------------------------------------------------------------------- /gwas_enrichment/calculate_treebased_snpcentric.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cboix/EPIMAP_ANALYSIS/HEAD/gwas_enrichment/calculate_treebased_snpcentric.R -------------------------------------------------------------------------------- /gwas_enrichment/count_snps_tree.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cboix/EPIMAP_ANALYSIS/HEAD/gwas_enrichment/count_snps_tree.R -------------------------------------------------------------------------------- /gwas_enrichment/count_unique_enriched_snps.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cboix/EPIMAP_ANALYSIS/HEAD/gwas_enrichment/count_unique_enriched_snps.R -------------------------------------------------------------------------------- /gwas_enrichment/gwas_plotting/calculate_all_flat_enrichments.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cboix/EPIMAP_ANALYSIS/HEAD/gwas_enrichment/gwas_plotting/calculate_all_flat_enrichments.R -------------------------------------------------------------------------------- /gwas_enrichment/gwas_plotting/calculate_all_gwastree_enrichments.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cboix/EPIMAP_ANALYSIS/HEAD/gwas_enrichment/gwas_plotting/calculate_all_gwastree_enrichments.R -------------------------------------------------------------------------------- /gwas_enrichment/gwas_plotting/calculate_gwastree_consensus.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cboix/EPIMAP_ANALYSIS/HEAD/gwas_enrichment/gwas_plotting/calculate_gwastree_consensus.R -------------------------------------------------------------------------------- /gwas_enrichment/gwas_plotting/calculate_gwastree_parsimony.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cboix/EPIMAP_ANALYSIS/HEAD/gwas_enrichment/gwas_plotting/calculate_gwastree_parsimony.R -------------------------------------------------------------------------------- /gwas_enrichment/gwas_plotting/create_gwas_intersect_matrix.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cboix/EPIMAP_ANALYSIS/HEAD/gwas_enrichment/gwas_plotting/create_gwas_intersect_matrix.sh -------------------------------------------------------------------------------- /gwas_enrichment/gwas_plotting/create_permuted_catalogs.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cboix/EPIMAP_ANALYSIS/HEAD/gwas_enrichment/gwas_plotting/create_permuted_catalogs.R -------------------------------------------------------------------------------- /gwas_enrichment/gwas_plotting/create_shuffled_full_catalogs.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cboix/EPIMAP_ANALYSIS/HEAD/gwas_enrichment/gwas_plotting/create_shuffled_full_catalogs.R -------------------------------------------------------------------------------- /gwas_enrichment/gwas_plotting/eval_gwastree_strategies.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cboix/EPIMAP_ANALYSIS/HEAD/gwas_enrichment/gwas_plotting/eval_gwastree_strategies.R -------------------------------------------------------------------------------- /gwas_enrichment/gwas_plotting/eval_pvalue_cutoffs.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cboix/EPIMAP_ANALYSIS/HEAD/gwas_enrichment/gwas_plotting/eval_pvalue_cutoffs.R -------------------------------------------------------------------------------- /gwas_enrichment/gwas_plotting/eval_pvalue_cutoffs_FWER.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cboix/EPIMAP_ANALYSIS/HEAD/gwas_enrichment/gwas_plotting/eval_pvalue_cutoffs_FWER.R -------------------------------------------------------------------------------- /gwas_enrichment/gwas_plotting/explore_gwastree_methodology.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cboix/EPIMAP_ANALYSIS/HEAD/gwas_enrichment/gwas_plotting/explore_gwastree_methodology.R -------------------------------------------------------------------------------- /gwas_enrichment/gwas_plotting/extract_gwastree_snp_intersections.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cboix/EPIMAP_ANALYSIS/HEAD/gwas_enrichment/gwas_plotting/extract_gwastree_snp_intersections.R -------------------------------------------------------------------------------- /gwas_enrichment/gwas_plotting/intersect_gwas_with_index.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cboix/EPIMAP_ANALYSIS/HEAD/gwas_enrichment/gwas_plotting/intersect_gwas_with_index.sh -------------------------------------------------------------------------------- /gwas_enrichment/gwas_plotting/plot_CAD_example_analysis.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cboix/EPIMAP_ANALYSIS/HEAD/gwas_enrichment/gwas_plotting/plot_CAD_example_analysis.R -------------------------------------------------------------------------------- /gwas_enrichment/gwas_plotting/plot_CAD_sumstats_qqplots.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cboix/EPIMAP_ANALYSIS/HEAD/gwas_enrichment/gwas_plotting/plot_CAD_sumstats_qqplots.R -------------------------------------------------------------------------------- /gwas_enrichment/gwas_plotting/plot_all_gwastree_example_analysis.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cboix/EPIMAP_ANALYSIS/HEAD/gwas_enrichment/gwas_plotting/plot_all_gwastree_example_analysis.R -------------------------------------------------------------------------------- /gwas_enrichment/gwas_plotting/plot_enrichments_gwastree.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cboix/EPIMAP_ANALYSIS/HEAD/gwas_enrichment/gwas_plotting/plot_enrichments_gwastree.R -------------------------------------------------------------------------------- /gwas_enrichment/gwas_plotting/plot_explore_main_gwastree_examples.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cboix/EPIMAP_ANALYSIS/HEAD/gwas_enrichment/gwas_plotting/plot_explore_main_gwastree_examples.R -------------------------------------------------------------------------------- /gwas_enrichment/gwas_plotting/plot_gwas_flathg_alone.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cboix/EPIMAP_ANALYSIS/HEAD/gwas_enrichment/gwas_plotting/plot_gwas_flathg_alone.R -------------------------------------------------------------------------------- /gwas_enrichment/gwas_plotting/plot_gwas_flathg_alone.log: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cboix/EPIMAP_ANALYSIS/HEAD/gwas_enrichment/gwas_plotting/plot_gwas_flathg_alone.log -------------------------------------------------------------------------------- /gwas_enrichment/gwas_plotting/plot_gwas_hg_stats_from_tables.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cboix/EPIMAP_ANALYSIS/HEAD/gwas_enrichment/gwas_plotting/plot_gwas_hg_stats_from_tables.R -------------------------------------------------------------------------------- /gwas_enrichment/gwas_plotting/plot_gwas_tree.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cboix/EPIMAP_ANALYSIS/HEAD/gwas_enrichment/gwas_plotting/plot_gwas_tree.R -------------------------------------------------------------------------------- /gwas_enrichment/gwas_plotting/plot_gwas_with_ML.ipynb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cboix/EPIMAP_ANALYSIS/HEAD/gwas_enrichment/gwas_plotting/plot_gwas_with_ML.ipynb -------------------------------------------------------------------------------- /gwas_enrichment/gwas_plotting/plot_gwastree_construction_methods.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cboix/EPIMAP_ANALYSIS/HEAD/gwas_enrichment/gwas_plotting/plot_gwastree_construction_methods.R -------------------------------------------------------------------------------- /gwas_enrichment/gwas_plotting/plot_gwastree_example_figures.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cboix/EPIMAP_ANALYSIS/HEAD/gwas_enrichment/gwas_plotting/plot_gwastree_example_figures.R -------------------------------------------------------------------------------- /gwas_enrichment/gwas_plotting/plot_gwastree_snp_intersections.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cboix/EPIMAP_ANALYSIS/HEAD/gwas_enrichment/gwas_plotting/plot_gwastree_snp_intersections.R -------------------------------------------------------------------------------- /gwas_enrichment/gwas_plotting/plot_gwastree_snp_loci.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cboix/EPIMAP_ANALYSIS/HEAD/gwas_enrichment/gwas_plotting/plot_gwastree_snp_loci.R -------------------------------------------------------------------------------- /gwas_enrichment/gwas_plotting/plot_gwastree_snp_loci_mainfigures.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cboix/EPIMAP_ANALYSIS/HEAD/gwas_enrichment/gwas_plotting/plot_gwastree_snp_loci_mainfigures.R -------------------------------------------------------------------------------- /gwas_enrichment/gwas_plotting/plot_gwastree_tissue_breakpoints.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cboix/EPIMAP_ANALYSIS/HEAD/gwas_enrichment/gwas_plotting/plot_gwastree_tissue_breakpoints.R -------------------------------------------------------------------------------- /gwas_enrichment/gwas_plotting/plot_statistics_gwas_gwastree_enrichments.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cboix/EPIMAP_ANALYSIS/HEAD/gwas_enrichment/gwas_plotting/plot_statistics_gwas_gwastree_enrichments.R -------------------------------------------------------------------------------- /gwas_enrichment/gwas_plotting/plot_statistics_tissue_gwastree_enrichments.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cboix/EPIMAP_ANALYSIS/HEAD/gwas_enrichment/gwas_plotting/plot_statistics_tissue_gwastree_enrichments.R -------------------------------------------------------------------------------- /gwas_enrichment/gwas_plotting/plot_statistics_validation_gwastree_enrichments.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cboix/EPIMAP_ANALYSIS/HEAD/gwas_enrichment/gwas_plotting/plot_statistics_validation_gwastree_enrichments.R -------------------------------------------------------------------------------- /gwas_enrichment/makefile: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cboix/EPIMAP_ANALYSIS/HEAD/gwas_enrichment/makefile -------------------------------------------------------------------------------- /gwas_enrichment/manifest.txt: -------------------------------------------------------------------------------- 1 | Main-Class: StateMWGwasPeakHyper 2 | -------------------------------------------------------------------------------- /gwas_enrichment/munge_CAD_example_sumstats.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cboix/EPIMAP_ANALYSIS/HEAD/gwas_enrichment/munge_CAD_example_sumstats.sh -------------------------------------------------------------------------------- /gwas_enrichment/plot_flat_hg_enr.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cboix/EPIMAP_ANALYSIS/HEAD/gwas_enrichment/plot_flat_hg_enr.R -------------------------------------------------------------------------------- /gwas_enrichment/plot_gwas_alone.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cboix/EPIMAP_ANALYSIS/HEAD/gwas_enrichment/plot_gwas_alone.R -------------------------------------------------------------------------------- /gwas_enrichment/plot_gwastree_gwas_network.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cboix/EPIMAP_ANALYSIS/HEAD/gwas_enrichment/plot_gwastree_gwas_network.R -------------------------------------------------------------------------------- /gwas_enrichment/plot_gwastree_small_figures.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cboix/EPIMAP_ANALYSIS/HEAD/gwas_enrichment/plot_gwastree_small_figures.R -------------------------------------------------------------------------------- /gwas_enrichment/run_gwas_hg_pipeline.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cboix/EPIMAP_ANALYSIS/HEAD/gwas_enrichment/run_gwas_hg_pipeline.sh -------------------------------------------------------------------------------- /ic_eval/aggregate_stats.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cboix/EPIMAP_ANALYSIS/HEAD/ic_eval/aggregate_stats.sh -------------------------------------------------------------------------------- /ic_eval/config_IC_files.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cboix/EPIMAP_ANALYSIS/HEAD/ic_eval/config_IC_files.sh -------------------------------------------------------------------------------- /ic_eval/imputation_pick_subset.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cboix/EPIMAP_ANALYSIS/HEAD/ic_eval/imputation_pick_subset.R -------------------------------------------------------------------------------- /ic_eval/plot_rank_IC_metrics.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cboix/EPIMAP_ANALYSIS/HEAD/ic_eval/plot_rank_IC_metrics.R -------------------------------------------------------------------------------- /ic_eval/process_IC_files.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cboix/EPIMAP_ANALYSIS/HEAD/ic_eval/process_IC_files.sh -------------------------------------------------------------------------------- /ic_eval/run_IC_eval.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cboix/EPIMAP_ANALYSIS/HEAD/ic_eval/run_IC_eval.sh -------------------------------------------------------------------------------- /ic_eval/run_IC_eval_pertrack.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cboix/EPIMAP_ANALYSIS/HEAD/ic_eval/run_IC_eval_pertrack.sh -------------------------------------------------------------------------------- /imputation_analysis/calculate_bwtrack_similarity.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cboix/EPIMAP_ANALYSIS/HEAD/imputation_analysis/calculate_bwtrack_similarity.py -------------------------------------------------------------------------------- /imputation_analysis/calculate_diff_of_datasets.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cboix/EPIMAP_ANALYSIS/HEAD/imputation_analysis/calculate_diff_of_datasets.py -------------------------------------------------------------------------------- /imputation_analysis/calculate_distance_of_datasets.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cboix/EPIMAP_ANALYSIS/HEAD/imputation_analysis/calculate_distance_of_datasets.py -------------------------------------------------------------------------------- /imputation_analysis/calculate_enhancer_matrix_umap.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cboix/EPIMAP_ANALYSIS/HEAD/imputation_analysis/calculate_enhancer_matrix_umap.py -------------------------------------------------------------------------------- /imputation_analysis/calculate_inc_pca.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cboix/EPIMAP_ANALYSIS/HEAD/imputation_analysis/calculate_inc_pca.py -------------------------------------------------------------------------------- /imputation_analysis/calculate_mark_average_tracks.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cboix/EPIMAP_ANALYSIS/HEAD/imputation_analysis/calculate_mark_average_tracks.py -------------------------------------------------------------------------------- /imputation_analysis/calculate_mark_recovery_metrics.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cboix/EPIMAP_ANALYSIS/HEAD/imputation_analysis/calculate_mark_recovery_metrics.py -------------------------------------------------------------------------------- /imputation_analysis/calculate_mark_variability.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cboix/EPIMAP_ANALYSIS/HEAD/imputation_analysis/calculate_mark_variability.py -------------------------------------------------------------------------------- /imputation_analysis/calculate_markmatrix_variability.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cboix/EPIMAP_ANALYSIS/HEAD/imputation_analysis/calculate_markmatrix_variability.py -------------------------------------------------------------------------------- /imputation_analysis/calculate_observed_emissions_overlap_chmm.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cboix/EPIMAP_ANALYSIS/HEAD/imputation_analysis/calculate_observed_emissions_overlap_chmm.R -------------------------------------------------------------------------------- /imputation_analysis/calculate_permuted_flat_enrichments.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cboix/EPIMAP_ANALYSIS/HEAD/imputation_analysis/calculate_permuted_flat_enrichments.R -------------------------------------------------------------------------------- /imputation_analysis/calculate_permuted_gwastree_enrichments.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cboix/EPIMAP_ANALYSIS/HEAD/imputation_analysis/calculate_permuted_gwastree_enrichments.R -------------------------------------------------------------------------------- /imputation_analysis/calculate_prune_enhmat.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cboix/EPIMAP_ANALYSIS/HEAD/imputation_analysis/calculate_prune_enhmat.R -------------------------------------------------------------------------------- /imputation_analysis/calculate_unexpected_genes_modules.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cboix/EPIMAP_ANALYSIS/HEAD/imputation_analysis/calculate_unexpected_genes_modules.R -------------------------------------------------------------------------------- /imputation_analysis/choose_rand_regions.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cboix/EPIMAP_ANALYSIS/HEAD/imputation_analysis/choose_rand_regions.R -------------------------------------------------------------------------------- /imputation_analysis/collate_chromimpute_distance.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cboix/EPIMAP_ANALYSIS/HEAD/imputation_analysis/collate_chromimpute_distance.sh -------------------------------------------------------------------------------- /imputation_analysis/compile_plot_eval_metrics.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cboix/EPIMAP_ANALYSIS/HEAD/imputation_analysis/compile_plot_eval_metrics.sh -------------------------------------------------------------------------------- /imputation_analysis/compute_IC_data_metrics.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cboix/EPIMAP_ANALYSIS/HEAD/imputation_analysis/compute_IC_data_metrics.R -------------------------------------------------------------------------------- /imputation_analysis/compute_coverage_overall_chromHMM.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cboix/EPIMAP_ANALYSIS/HEAD/imputation_analysis/compute_coverage_overall_chromHMM.sh -------------------------------------------------------------------------------- /imputation_analysis/convert_IC_data_hg19_fixedstep.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cboix/EPIMAP_ANALYSIS/HEAD/imputation_analysis/convert_IC_data_hg19_fixedstep.sh -------------------------------------------------------------------------------- /imputation_analysis/plot_IC_data_metrics.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cboix/EPIMAP_ANALYSIS/HEAD/imputation_analysis/plot_IC_data_metrics.R -------------------------------------------------------------------------------- /imputation_analysis/plot_IC_signal_distribution.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cboix/EPIMAP_ANALYSIS/HEAD/imputation_analysis/plot_IC_signal_distribution.R -------------------------------------------------------------------------------- /imputation_analysis/plot_aggregate_stats_bwpk.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cboix/EPIMAP_ANALYSIS/HEAD/imputation_analysis/plot_aggregate_stats_bwpk.R -------------------------------------------------------------------------------- /imputation_analysis/plot_chromHMM_frequencies.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cboix/EPIMAP_ANALYSIS/HEAD/imputation_analysis/plot_chromHMM_frequencies.R -------------------------------------------------------------------------------- /imputation_analysis/plot_chromHMM_region.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cboix/EPIMAP_ANALYSIS/HEAD/imputation_analysis/plot_chromHMM_region.R -------------------------------------------------------------------------------- /imputation_analysis/plot_chromImpute_diff_qc.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cboix/EPIMAP_ANALYSIS/HEAD/imputation_analysis/plot_chromImpute_diff_qc.R -------------------------------------------------------------------------------- /imputation_analysis/plot_chromImpute_distance.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cboix/EPIMAP_ANALYSIS/HEAD/imputation_analysis/plot_chromImpute_distance.R -------------------------------------------------------------------------------- /imputation_analysis/plot_chromImpute_imputed_distance.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cboix/EPIMAP_ANALYSIS/HEAD/imputation_analysis/plot_chromImpute_imputed_distance.R -------------------------------------------------------------------------------- /imputation_analysis/plot_chromImpute_imputed_trees.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cboix/EPIMAP_ANALYSIS/HEAD/imputation_analysis/plot_chromImpute_imputed_trees.R -------------------------------------------------------------------------------- /imputation_analysis/plot_chromImpute_imputed_umap.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cboix/EPIMAP_ANALYSIS/HEAD/imputation_analysis/plot_chromImpute_imputed_umap.R -------------------------------------------------------------------------------- /imputation_analysis/plot_chromImpute_imputed_umap_homogeneity.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cboix/EPIMAP_ANALYSIS/HEAD/imputation_analysis/plot_chromImpute_imputed_umap_homogeneity.R -------------------------------------------------------------------------------- /imputation_analysis/plot_chromImpute_metrics.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cboix/EPIMAP_ANALYSIS/HEAD/imputation_analysis/plot_chromImpute_metrics.R -------------------------------------------------------------------------------- /imputation_analysis/plot_chromImpute_metrics_bysupport.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cboix/EPIMAP_ANALYSIS/HEAD/imputation_analysis/plot_chromImpute_metrics_bysupport.R -------------------------------------------------------------------------------- /imputation_analysis/plot_chromImpute_metrics_final.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cboix/EPIMAP_ANALYSIS/HEAD/imputation_analysis/plot_chromImpute_metrics_final.R -------------------------------------------------------------------------------- /imputation_analysis/plot_chromImpute_signal_distributions.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cboix/EPIMAP_ANALYSIS/HEAD/imputation_analysis/plot_chromImpute_signal_distributions.R -------------------------------------------------------------------------------- /imputation_analysis/plot_clusters_motifs.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cboix/EPIMAP_ANALYSIS/HEAD/imputation_analysis/plot_clusters_motifs.R -------------------------------------------------------------------------------- /imputation_analysis/plot_datamatrix.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cboix/EPIMAP_ANALYSIS/HEAD/imputation_analysis/plot_datamatrix.R -------------------------------------------------------------------------------- /imputation_analysis/plot_dataorigin.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cboix/EPIMAP_ANALYSIS/HEAD/imputation_analysis/plot_dataorigin.R -------------------------------------------------------------------------------- /imputation_analysis/plot_datashader_matrix.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cboix/EPIMAP_ANALYSIS/HEAD/imputation_analysis/plot_datashader_matrix.py -------------------------------------------------------------------------------- /imputation_analysis/plot_eval_diff_secondary.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cboix/EPIMAP_ANALYSIS/HEAD/imputation_analysis/plot_eval_diff_secondary.R -------------------------------------------------------------------------------- /imputation_analysis/plot_eval_sampswaps.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cboix/EPIMAP_ANALYSIS/HEAD/imputation_analysis/plot_eval_sampswaps.R -------------------------------------------------------------------------------- /imputation_analysis/plot_example_impobs_nuc_regions.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cboix/EPIMAP_ANALYSIS/HEAD/imputation_analysis/plot_example_impobs_nuc_regions.R -------------------------------------------------------------------------------- /imputation_analysis/plot_impobs_groups.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cboix/EPIMAP_ANALYSIS/HEAD/imputation_analysis/plot_impobs_groups.R -------------------------------------------------------------------------------- /imputation_analysis/plot_impobs_tracks.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cboix/EPIMAP_ANALYSIS/HEAD/imputation_analysis/plot_impobs_tracks.R -------------------------------------------------------------------------------- /imputation_analysis/plot_linked_enrichments_gwastree.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cboix/EPIMAP_ANALYSIS/HEAD/imputation_analysis/plot_linked_enrichments_gwastree.R -------------------------------------------------------------------------------- /imputation_analysis/plot_linking_02_corr_examples.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cboix/EPIMAP_ANALYSIS/HEAD/imputation_analysis/plot_linking_02_corr_examples.R -------------------------------------------------------------------------------- /imputation_analysis/plot_linking_03_localNMF_test.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cboix/EPIMAP_ANALYSIS/HEAD/imputation_analysis/plot_linking_03_localNMF_test.R -------------------------------------------------------------------------------- /imputation_analysis/plot_linking_04_make_corr_fdr_pred.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cboix/EPIMAP_ANALYSIS/HEAD/imputation_analysis/plot_linking_04_make_corr_fdr_pred.R -------------------------------------------------------------------------------- /imputation_analysis/plot_linking_05_goenrichment.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cboix/EPIMAP_ANALYSIS/HEAD/imputation_analysis/plot_linking_05_goenrichment.R -------------------------------------------------------------------------------- /imputation_analysis/plot_linking_06_validation_figures.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cboix/EPIMAP_ANALYSIS/HEAD/imputation_analysis/plot_linking_06_validation_figures.R -------------------------------------------------------------------------------- /imputation_analysis/plot_modules_3panelsubsets.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cboix/EPIMAP_ANALYSIS/HEAD/imputation_analysis/plot_modules_3panelsubsets.R -------------------------------------------------------------------------------- /imputation_analysis/plot_modules_obsvalidation.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cboix/EPIMAP_ANALYSIS/HEAD/imputation_analysis/plot_modules_obsvalidation.R -------------------------------------------------------------------------------- /imputation_analysis/plot_modules_only.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cboix/EPIMAP_ANALYSIS/HEAD/imputation_analysis/plot_modules_only.R -------------------------------------------------------------------------------- /imputation_analysis/plot_modules_with_fimo.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cboix/EPIMAP_ANALYSIS/HEAD/imputation_analysis/plot_modules_with_fimo.R -------------------------------------------------------------------------------- /imputation_analysis/plot_modules_with_great.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cboix/EPIMAP_ANALYSIS/HEAD/imputation_analysis/plot_modules_with_great.R -------------------------------------------------------------------------------- /imputation_analysis/plot_modules_with_gwas.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cboix/EPIMAP_ANALYSIS/HEAD/imputation_analysis/plot_modules_with_gwas.R -------------------------------------------------------------------------------- /imputation_analysis/plot_modules_with_gwas_flathg.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cboix/EPIMAP_ANALYSIS/HEAD/imputation_analysis/plot_modules_with_gwas_flathg.R -------------------------------------------------------------------------------- /imputation_analysis/plot_modules_with_motifs.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cboix/EPIMAP_ANALYSIS/HEAD/imputation_analysis/plot_modules_with_motifs.R -------------------------------------------------------------------------------- /imputation_analysis/plot_motifs_alone.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cboix/EPIMAP_ANALYSIS/HEAD/imputation_analysis/plot_motifs_alone.R -------------------------------------------------------------------------------- /imputation_analysis/plot_motifs_epigenomes_network.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cboix/EPIMAP_ANALYSIS/HEAD/imputation_analysis/plot_motifs_epigenomes_network.R -------------------------------------------------------------------------------- /imputation_analysis/plot_observed_emissions_overlap_chmm.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cboix/EPIMAP_ANALYSIS/HEAD/imputation_analysis/plot_observed_emissions_overlap_chmm.R -------------------------------------------------------------------------------- /imputation_analysis/plot_own_masterlist_statistics.ipynb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cboix/EPIMAP_ANALYSIS/HEAD/imputation_analysis/plot_own_masterlist_statistics.ipynb -------------------------------------------------------------------------------- /imputation_analysis/plot_rand_regions.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cboix/EPIMAP_ANALYSIS/HEAD/imputation_analysis/plot_rand_regions.R -------------------------------------------------------------------------------- /imputation_analysis/plot_reads_distribution.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cboix/EPIMAP_ANALYSIS/HEAD/imputation_analysis/plot_reads_distribution.R -------------------------------------------------------------------------------- /imputation_analysis/plot_sample_mark_chromImpute.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cboix/EPIMAP_ANALYSIS/HEAD/imputation_analysis/plot_sample_mark_chromImpute.R -------------------------------------------------------------------------------- /imputation_analysis/plot_stats_bw_pk_intersection.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cboix/EPIMAP_ANALYSIS/HEAD/imputation_analysis/plot_stats_bw_pk_intersection.R -------------------------------------------------------------------------------- /imputation_analysis/plot_vplot.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cboix/EPIMAP_ANALYSIS/HEAD/imputation_analysis/plot_vplot.py -------------------------------------------------------------------------------- /imputation_analysis/prioritize_diff_tracks.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cboix/EPIMAP_ANALYSIS/HEAD/imputation_analysis/prioritize_diff_tracks.R -------------------------------------------------------------------------------- /imputation_analysis/promoter_stats.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cboix/EPIMAP_ANALYSIS/HEAD/imputation_analysis/promoter_stats.R -------------------------------------------------------------------------------- /imputation_analysis/query_motif_DHSlist.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cboix/EPIMAP_ANALYSIS/HEAD/imputation_analysis/query_motif_DHSlist.R -------------------------------------------------------------------------------- /imputation_analysis/reduce_intersect_GTEx_eQTLs.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cboix/EPIMAP_ANALYSIS/HEAD/imputation_analysis/reduce_intersect_GTEx_eQTLs.sh -------------------------------------------------------------------------------- /imputation_analysis/uncertainty_analysis/compare_uncertainty_01_plot_tracks.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cboix/EPIMAP_ANALYSIS/HEAD/imputation_analysis/uncertainty_analysis/compare_uncertainty_01_plot_tracks.R -------------------------------------------------------------------------------- /imputation_analysis/uncertainty_analysis/compare_uncertainty_02_coeffv_vs_mark.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cboix/EPIMAP_ANALYSIS/HEAD/imputation_analysis/uncertainty_analysis/compare_uncertainty_02_coeffv_vs_mark.R -------------------------------------------------------------------------------- /imputation_analysis/uncertainty_analysis/compare_uncertainty_03_mark_matrices.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cboix/EPIMAP_ANALYSIS/HEAD/imputation_analysis/uncertainty_analysis/compare_uncertainty_03_mark_matrices.R -------------------------------------------------------------------------------- /imputation_analysis/uncertainty_analysis/compare_uncertainty_04_dnase_enhancer_intersect.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cboix/EPIMAP_ANALYSIS/HEAD/imputation_analysis/uncertainty_analysis/compare_uncertainty_04_dnase_enhancer_intersect.R -------------------------------------------------------------------------------- /imputation_analysis/uncertainty_analysis/compare_uncertainty_05_mark_recovery_metrics.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cboix/EPIMAP_ANALYSIS/HEAD/imputation_analysis/uncertainty_analysis/compare_uncertainty_05_mark_recovery_metrics.R -------------------------------------------------------------------------------- /imputation_analysis/uncertainty_analysis/compare_uncertainty_06_dhs_recovery_metrics.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cboix/EPIMAP_ANALYSIS/HEAD/imputation_analysis/uncertainty_analysis/compare_uncertainty_06_dhs_recovery_metrics.R -------------------------------------------------------------------------------- /imputation_analysis/uncertainty_analysis/compare_uncertainty_07_nondhs_recovery_metrics.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cboix/EPIMAP_ANALYSIS/HEAD/imputation_analysis/uncertainty_analysis/compare_uncertainty_07_nondhs_recovery_metrics.R -------------------------------------------------------------------------------- /impute_vis/data/DataSummary_ordered_distances.tsv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cboix/EPIMAP_ANALYSIS/HEAD/impute_vis/data/DataSummary_ordered_distances.tsv -------------------------------------------------------------------------------- /impute_vis/data/DataSummary_ordered_table.tsv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cboix/EPIMAP_ANALYSIS/HEAD/impute_vis/data/DataSummary_ordered_table.tsv -------------------------------------------------------------------------------- /impute_vis/data/celltypes.tsv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cboix/EPIMAP_ANALYSIS/HEAD/impute_vis/data/celltypes.tsv -------------------------------------------------------------------------------- /impute_vis/data/new_samples_mapping.tsv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cboix/EPIMAP_ANALYSIS/HEAD/impute_vis/data/new_samples_mapping.tsv -------------------------------------------------------------------------------- /impute_vis/imputation_avail_funcs.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cboix/EPIMAP_ANALYSIS/HEAD/impute_vis/imputation_avail_funcs.R -------------------------------------------------------------------------------- /impute_vis/server.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cboix/EPIMAP_ANALYSIS/HEAD/impute_vis/server.R -------------------------------------------------------------------------------- /impute_vis/ui.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cboix/EPIMAP_ANALYSIS/HEAD/impute_vis/ui.R -------------------------------------------------------------------------------- /ldsc_enrichment/process_bed_to_annot.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cboix/EPIMAP_ANALYSIS/HEAD/ldsc_enrichment/process_bed_to_annot.sh -------------------------------------------------------------------------------- /ldsc_enrichment/process_gwas_dir_leadsnps.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cboix/EPIMAP_ANALYSIS/HEAD/ldsc_enrichment/process_gwas_dir_leadsnps.sh -------------------------------------------------------------------------------- /ldsc_enrichment/process_gwas_dir_sumstats.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cboix/EPIMAP_ANALYSIS/HEAD/ldsc_enrichment/process_gwas_dir_sumstats.sh -------------------------------------------------------------------------------- /ldsc_enrichment/prune_leadsnps.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cboix/EPIMAP_ANALYSIS/HEAD/ldsc_enrichment/prune_leadsnps.py -------------------------------------------------------------------------------- /ldsc_enrichment/run_partition_heritability_per_gwas.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cboix/EPIMAP_ANALYSIS/HEAD/ldsc_enrichment/run_partition_heritability_per_gwas.sh -------------------------------------------------------------------------------- /ldsc_enrichment/submit_ldsc_pipeline.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cboix/EPIMAP_ANALYSIS/HEAD/ldsc_enrichment/submit_ldsc_pipeline.sh -------------------------------------------------------------------------------- /ldsc_enrichment/submit_process_gwas_dir_sumstats.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cboix/EPIMAP_ANALYSIS/HEAD/ldsc_enrichment/submit_process_gwas_dir_sumstats.sh -------------------------------------------------------------------------------- /linking_methods/Roadmap_Linking_YLiu.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cboix/EPIMAP_ANALYSIS/HEAD/linking_methods/Roadmap_Linking_YLiu.java -------------------------------------------------------------------------------- /load_distance_matrices.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cboix/EPIMAP_ANALYSIS/HEAD/load_distance_matrices.R -------------------------------------------------------------------------------- /load_gwastree_analysis.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cboix/EPIMAP_ANALYSIS/HEAD/load_gwastree_analysis.R -------------------------------------------------------------------------------- /load_linking_data.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cboix/EPIMAP_ANALYSIS/HEAD/load_linking_data.py -------------------------------------------------------------------------------- /load_linking_objects.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cboix/EPIMAP_ANALYSIS/HEAD/load_linking_objects.R -------------------------------------------------------------------------------- /load_metadata.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cboix/EPIMAP_ANALYSIS/HEAD/load_metadata.R -------------------------------------------------------------------------------- /load_modules_data.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cboix/EPIMAP_ANALYSIS/HEAD/load_modules_data.R -------------------------------------------------------------------------------- /load_region_distance_matrices.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cboix/EPIMAP_ANALYSIS/HEAD/load_region_distance_matrices.R -------------------------------------------------------------------------------- /load_statistics_gwastree_enrichments.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cboix/EPIMAP_ANALYSIS/HEAD/load_statistics_gwastree_enrichments.R -------------------------------------------------------------------------------- /load_updated_validation_enrichments.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cboix/EPIMAP_ANALYSIS/HEAD/load_updated_validation_enrichments.R -------------------------------------------------------------------------------- /load_validation_gwastree_enrichments.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cboix/EPIMAP_ANALYSIS/HEAD/load_validation_gwastree_enrichments.R -------------------------------------------------------------------------------- /main_EPIMAP_ANALYSIS.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cboix/EPIMAP_ANALYSIS/HEAD/main_EPIMAP_ANALYSIS.R -------------------------------------------------------------------------------- /meme_enrichment/aggregate_parsed_fimo_results.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cboix/EPIMAP_ANALYSIS/HEAD/meme_enrichment/aggregate_parsed_fimo_results.R -------------------------------------------------------------------------------- /meme_enrichment/aggregate_raw_fimo_results.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cboix/EPIMAP_ANALYSIS/HEAD/meme_enrichment/aggregate_raw_fimo_results.R -------------------------------------------------------------------------------- /meme_enrichment/parse_fimo_results.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cboix/EPIMAP_ANALYSIS/HEAD/meme_enrichment/parse_fimo_results.R -------------------------------------------------------------------------------- /meme_enrichment/plot_fimo_alone.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cboix/EPIMAP_ANALYSIS/HEAD/meme_enrichment/plot_fimo_alone.R -------------------------------------------------------------------------------- /meme_enrichment/run_fimo.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cboix/EPIMAP_ANALYSIS/HEAD/meme_enrichment/run_fimo.sh -------------------------------------------------------------------------------- /meme_enrichment/run_fimo_db.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cboix/EPIMAP_ANALYSIS/HEAD/meme_enrichment/run_fimo_db.sh -------------------------------------------------------------------------------- /meme_enrichment/submit_fimo_enrichment.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cboix/EPIMAP_ANALYSIS/HEAD/meme_enrichment/submit_fimo_enrichment.sh -------------------------------------------------------------------------------- /metadata_scripts/choose_expression_files.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cboix/EPIMAP_ANALYSIS/HEAD/metadata_scripts/choose_expression_files.R -------------------------------------------------------------------------------- /metadata_scripts/get_RNAseq_microarray_ENCODE.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cboix/EPIMAP_ANALYSIS/HEAD/metadata_scripts/get_RNAseq_microarray_ENCODE.R -------------------------------------------------------------------------------- /metadata_scripts/get_available_ENCODE_links.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cboix/EPIMAP_ANALYSIS/HEAD/metadata_scripts/get_available_ENCODE_links.R -------------------------------------------------------------------------------- /metadata_scripts/get_experiments_ENCODE.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cboix/EPIMAP_ANALYSIS/HEAD/metadata_scripts/get_experiments_ENCODE.R -------------------------------------------------------------------------------- /metadata_scripts/get_metadata_ENCODE.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cboix/EPIMAP_ANALYSIS/HEAD/metadata_scripts/get_metadata_ENCODE.R -------------------------------------------------------------------------------- /metadata_scripts/get_roadmap_mapping.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cboix/EPIMAP_ANALYSIS/HEAD/metadata_scripts/get_roadmap_mapping.R -------------------------------------------------------------------------------- /metadata_scripts/imputation_avail_funcs.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cboix/EPIMAP_ANALYSIS/HEAD/metadata_scripts/imputation_avail_funcs.R -------------------------------------------------------------------------------- /metadata_scripts/imputation_availability_table.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cboix/EPIMAP_ANALYSIS/HEAD/metadata_scripts/imputation_availability_table.R -------------------------------------------------------------------------------- /metadata_scripts/make_trackhub_average_bigwigs.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cboix/EPIMAP_ANALYSIS/HEAD/metadata_scripts/make_trackhub_average_bigwigs.R -------------------------------------------------------------------------------- /metadata_scripts/make_trackhub_bigwigs.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cboix/EPIMAP_ANALYSIS/HEAD/metadata_scripts/make_trackhub_bigwigs.R -------------------------------------------------------------------------------- /metadata_scripts/make_trackhub_chromHMM.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cboix/EPIMAP_ANALYSIS/HEAD/metadata_scripts/make_trackhub_chromHMM.R -------------------------------------------------------------------------------- /metadata_scripts/make_trackhub_pergroup.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cboix/EPIMAP_ANALYSIS/HEAD/metadata_scripts/make_trackhub_pergroup.R -------------------------------------------------------------------------------- /motif_enrichment/compute_motif_enrichment.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cboix/EPIMAP_ANALYSIS/HEAD/motif_enrichment/compute_motif_enrichment.py -------------------------------------------------------------------------------- /motif_enrichment/count_regions_bkg_motifs.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cboix/EPIMAP_ANALYSIS/HEAD/motif_enrichment/count_regions_bkg_motifs.py -------------------------------------------------------------------------------- /motif_enrichment/motif_shuffle.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cboix/EPIMAP_ANALYSIS/HEAD/motif_enrichment/motif_shuffle.py -------------------------------------------------------------------------------- /motif_enrichment/plot_basic_motifs.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cboix/EPIMAP_ANALYSIS/HEAD/motif_enrichment/plot_basic_motifs.R -------------------------------------------------------------------------------- /motif_enrichment/plot_motif_logos.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cboix/EPIMAP_ANALYSIS/HEAD/motif_enrichment/plot_motif_logos.R -------------------------------------------------------------------------------- /motif_enrichment/reduce_motif_matches.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cboix/EPIMAP_ANALYSIS/HEAD/motif_enrichment/reduce_motif_matches.sh -------------------------------------------------------------------------------- /motif_enrichment/run_motif_matches.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cboix/EPIMAP_ANALYSIS/HEAD/motif_enrichment/run_motif_matches.sh -------------------------------------------------------------------------------- /motif_enrichment/run_regions_bkg_comparison.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cboix/EPIMAP_ANALYSIS/HEAD/motif_enrichment/run_regions_bkg_comparison.sh -------------------------------------------------------------------------------- /motif_enrichment/submit_motif_enrichment_pipe.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cboix/EPIMAP_ANALYSIS/HEAD/motif_enrichment/submit_motif_enrichment_pipe.sh -------------------------------------------------------------------------------- /motif_enrichment/submit_regions_bkg_comparison.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cboix/EPIMAP_ANALYSIS/HEAD/motif_enrichment/submit_regions_bkg_comparison.sh -------------------------------------------------------------------------------- /motifassoc_analysis/calculate_motif_matrix.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cboix/EPIMAP_ANALYSIS/HEAD/motifassoc_analysis/calculate_motif_matrix.R -------------------------------------------------------------------------------- /old_preprocessing_scripts/ATAC_pipeline.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cboix/EPIMAP_ANALYSIS/HEAD/old_preprocessing_scripts/ATAC_pipeline.sh -------------------------------------------------------------------------------- /old_preprocessing_scripts/BAMtoTA_download_preprocess.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cboix/EPIMAP_ANALYSIS/HEAD/old_preprocessing_scripts/BAMtoTA_download_preprocess.sh -------------------------------------------------------------------------------- /old_preprocessing_scripts/Call_peaks.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cboix/EPIMAP_ANALYSIS/HEAD/old_preprocessing_scripts/Call_peaks.sh -------------------------------------------------------------------------------- /old_preprocessing_scripts/ChIP_pipeline.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cboix/EPIMAP_ANALYSIS/HEAD/old_preprocessing_scripts/ChIP_pipeline.sh -------------------------------------------------------------------------------- /old_preprocessing_scripts/DNase_compute_window_occupancy.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cboix/EPIMAP_ANALYSIS/HEAD/old_preprocessing_scripts/DNase_compute_window_occupancy.sh -------------------------------------------------------------------------------- /old_preprocessing_scripts/DNase_download_preprocess.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cboix/EPIMAP_ANALYSIS/HEAD/old_preprocessing_scripts/DNase_download_preprocess.sh -------------------------------------------------------------------------------- /old_preprocessing_scripts/Generate_signal_tracks.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cboix/EPIMAP_ANALYSIS/HEAD/old_preprocessing_scripts/Generate_signal_tracks.sh -------------------------------------------------------------------------------- /old_preprocessing_scripts/Pool_subsample_SCCA.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cboix/EPIMAP_ANALYSIS/HEAD/old_preprocessing_scripts/Pool_subsample_SCCA.sh -------------------------------------------------------------------------------- /old_preprocessing_scripts/by_header.awk: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cboix/EPIMAP_ANALYSIS/HEAD/old_preprocessing_scripts/by_header.awk -------------------------------------------------------------------------------- /old_preprocessing_scripts/check_procfiles.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cboix/EPIMAP_ANALYSIS/HEAD/old_preprocessing_scripts/check_procfiles.sh -------------------------------------------------------------------------------- /old_preprocessing_scripts/collate_expression_tsv.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cboix/EPIMAP_ANALYSIS/HEAD/old_preprocessing_scripts/collate_expression_tsv.sh -------------------------------------------------------------------------------- /old_preprocessing_scripts/determine_resampling_performance.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cboix/EPIMAP_ANALYSIS/HEAD/old_preprocessing_scripts/determine_resampling_performance.sh -------------------------------------------------------------------------------- /old_preprocessing_scripts/distance_between_binned.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cboix/EPIMAP_ANALYSIS/HEAD/old_preprocessing_scripts/distance_between_binned.sh -------------------------------------------------------------------------------- /old_preprocessing_scripts/distance_from_contingency.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cboix/EPIMAP_ANALYSIS/HEAD/old_preprocessing_scripts/distance_from_contingency.R -------------------------------------------------------------------------------- /old_preprocessing_scripts/get_DNase_data.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cboix/EPIMAP_ANALYSIS/HEAD/old_preprocessing_scripts/get_DNase_data.sh -------------------------------------------------------------------------------- /old_preprocessing_scripts/get_IHEC_histone_bw_tracks.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cboix/EPIMAP_ANALYSIS/HEAD/old_preprocessing_scripts/get_IHEC_histone_bw_tracks.sh -------------------------------------------------------------------------------- /old_preprocessing_scripts/get_roadmap_enh.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cboix/EPIMAP_ANALYSIS/HEAD/old_preprocessing_scripts/get_roadmap_enh.sh -------------------------------------------------------------------------------- /old_preprocessing_scripts/make_contingency_table_for_binned.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cboix/EPIMAP_ANALYSIS/HEAD/old_preprocessing_scripts/make_contingency_table_for_binned.sh -------------------------------------------------------------------------------- /old_preprocessing_scripts/metrics_resampled_data.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cboix/EPIMAP_ANALYSIS/HEAD/old_preprocessing_scripts/metrics_resampled_data.sh -------------------------------------------------------------------------------- /old_preprocessing_scripts/plot_processing_status.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cboix/EPIMAP_ANALYSIS/HEAD/old_preprocessing_scripts/plot_processing_status.R -------------------------------------------------------------------------------- /old_preprocessing_scripts/plot_relevant_ChIPseq_expt.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cboix/EPIMAP_ANALYSIS/HEAD/old_preprocessing_scripts/plot_relevant_ChIPseq_expt.R -------------------------------------------------------------------------------- /old_preprocessing_scripts/read_bw.cpp: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cboix/EPIMAP_ANALYSIS/HEAD/old_preprocessing_scripts/read_bw.cpp -------------------------------------------------------------------------------- /old_preprocessing_scripts/run_ChIP_epitope.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cboix/EPIMAP_ANALYSIS/HEAD/old_preprocessing_scripts/run_ChIP_epitope.sh -------------------------------------------------------------------------------- /old_preprocessing_scripts/run_ChIP_epitope_cell.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cboix/EPIMAP_ANALYSIS/HEAD/old_preprocessing_scripts/run_ChIP_epitope_cell.sh -------------------------------------------------------------------------------- /old_preprocessing_scripts/run_ChIP_parallel.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cboix/EPIMAP_ANALYSIS/HEAD/old_preprocessing_scripts/run_ChIP_parallel.sh -------------------------------------------------------------------------------- /old_preprocessing_scripts/run_DNase_pipeline.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cboix/EPIMAP_ANALYSIS/HEAD/old_preprocessing_scripts/run_DNase_pipeline.sh -------------------------------------------------------------------------------- /old_preprocessing_scripts/run_single_files.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cboix/EPIMAP_ANALYSIS/HEAD/old_preprocessing_scripts/run_single_files.sh -------------------------------------------------------------------------------- /old_preprocessing_scripts/single_rep_peaks_signal.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cboix/EPIMAP_ANALYSIS/HEAD/old_preprocessing_scripts/single_rep_peaks_signal.sh -------------------------------------------------------------------------------- /postprocessing_scripts/convert_chmm_mat.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cboix/EPIMAP_ANALYSIS/HEAD/postprocessing_scripts/convert_chmm_mat.sh -------------------------------------------------------------------------------- /postprocessing_scripts/make_ChromHMM_bigbed_tracks.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cboix/EPIMAP_ANALYSIS/HEAD/postprocessing_scripts/make_ChromHMM_bigbed_tracks.sh -------------------------------------------------------------------------------- /postprocessing_scripts/make_and_transfer_bw_for_release.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cboix/EPIMAP_ANALYSIS/HEAD/postprocessing_scripts/make_and_transfer_bw_for_release.sh -------------------------------------------------------------------------------- /postprocessing_scripts/make_average_bw_for_release.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cboix/EPIMAP_ANALYSIS/HEAD/postprocessing_scripts/make_average_bw_for_release.sh -------------------------------------------------------------------------------- /postprocessing_scripts/make_bw_for_release.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cboix/EPIMAP_ANALYSIS/HEAD/postprocessing_scripts/make_bw_for_release.sh -------------------------------------------------------------------------------- /postprocessing_scripts/merge_DHS_sites_public.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cboix/EPIMAP_ANALYSIS/HEAD/postprocessing_scripts/merge_DHS_sites_public.R -------------------------------------------------------------------------------- /postprocessing_scripts/print_split_enh_out.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cboix/EPIMAP_ANALYSIS/HEAD/postprocessing_scripts/print_split_enh_out.R -------------------------------------------------------------------------------- /preprocessing_pipeline/.gitignore: -------------------------------------------------------------------------------- 1 | .snakemake/ 2 | __pycache__/ 3 | -------------------------------------------------------------------------------- /preprocessing_pipeline/check_for_completion.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cboix/EPIMAP_ANALYSIS/HEAD/preprocessing_pipeline/check_for_completion.sh -------------------------------------------------------------------------------- /preprocessing_pipeline/clean_empty_tagAligns.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cboix/EPIMAP_ANALYSIS/HEAD/preprocessing_pipeline/clean_empty_tagAligns.sh -------------------------------------------------------------------------------- /preprocessing_pipeline/clean_procfiles.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cboix/EPIMAP_ANALYSIS/HEAD/preprocessing_pipeline/clean_procfiles.sh -------------------------------------------------------------------------------- /preprocessing_pipeline/collate_CR_datasets.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cboix/EPIMAP_ANALYSIS/HEAD/preprocessing_pipeline/collate_CR_datasets.sh -------------------------------------------------------------------------------- /preprocessing_pipeline/collate_DHS_windows.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cboix/EPIMAP_ANALYSIS/HEAD/preprocessing_pipeline/collate_DHS_windows.sh -------------------------------------------------------------------------------- /preprocessing_pipeline/config.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cboix/EPIMAP_ANALYSIS/HEAD/preprocessing_pipeline/config.py -------------------------------------------------------------------------------- /preprocessing_pipeline/general.snake: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cboix/EPIMAP_ANALYSIS/HEAD/preprocessing_pipeline/general.snake -------------------------------------------------------------------------------- /preprocessing_pipeline/generate_processing_status_report.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cboix/EPIMAP_ANALYSIS/HEAD/preprocessing_pipeline/generate_processing_status_report.sh -------------------------------------------------------------------------------- /preprocessing_pipeline/process_normalize_qc_RNAseq.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cboix/EPIMAP_ANALYSIS/HEAD/preprocessing_pipeline/process_normalize_qc_RNAseq.R -------------------------------------------------------------------------------- /preprocessing_pipeline/project.snake: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cboix/EPIMAP_ANALYSIS/HEAD/preprocessing_pipeline/project.snake -------------------------------------------------------------------------------- /preprocessing_pipeline/rules/BAMtoTA_download_preprocess.rules: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cboix/EPIMAP_ANALYSIS/HEAD/preprocessing_pipeline/rules/BAMtoTA_download_preprocess.rules -------------------------------------------------------------------------------- /preprocessing_pipeline/rules/call_peaks_macs.rules: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cboix/EPIMAP_ANALYSIS/HEAD/preprocessing_pipeline/rules/call_peaks_macs.rules -------------------------------------------------------------------------------- /preprocessing_pipeline/rules/compute_window_occupancy.rules: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cboix/EPIMAP_ANALYSIS/HEAD/preprocessing_pipeline/rules/compute_window_occupancy.rules -------------------------------------------------------------------------------- /preprocessing_pipeline/rules/generate_signal_tracks_macs.rules: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cboix/EPIMAP_ANALYSIS/HEAD/preprocessing_pipeline/rules/generate_signal_tracks_macs.rules -------------------------------------------------------------------------------- /preprocessing_pipeline/rules/pool_subsample_SCCA.rules: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cboix/EPIMAP_ANALYSIS/HEAD/preprocessing_pipeline/rules/pool_subsample_SCCA.rules -------------------------------------------------------------------------------- /preprocessing_pipeline/run_TF_epitopes.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cboix/EPIMAP_ANALYSIS/HEAD/preprocessing_pipeline/run_TF_epitopes.sh -------------------------------------------------------------------------------- /preprocessing_pipeline/run_minor_jobs.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cboix/EPIMAP_ANALYSIS/HEAD/preprocessing_pipeline/run_minor_jobs.sh -------------------------------------------------------------------------------- /preprocessing_pipeline/run_snakemake.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cboix/EPIMAP_ANALYSIS/HEAD/preprocessing_pipeline/run_snakemake.sh -------------------------------------------------------------------------------- /preprocessing_pipeline/submit_project_parallel.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cboix/EPIMAP_ANALYSIS/HEAD/preprocessing_pipeline/submit_project_parallel.sh -------------------------------------------------------------------------------- /preprocessing_pipeline/submit_snakemake_parallel.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cboix/EPIMAP_ANALYSIS/HEAD/preprocessing_pipeline/submit_snakemake_parallel.sh -------------------------------------------------------------------------------- /screen_comparison/compare_to_screen_dels_01_overlap.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cboix/EPIMAP_ANALYSIS/HEAD/screen_comparison/compare_to_screen_dels_01_overlap.R -------------------------------------------------------------------------------- /screen_comparison/compare_to_screen_dels_02_gwas.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cboix/EPIMAP_ANALYSIS/HEAD/screen_comparison/compare_to_screen_dels_02_gwas.R -------------------------------------------------------------------------------- /setup_scripts/get_mappability_tracks.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cboix/EPIMAP_ANALYSIS/HEAD/setup_scripts/get_mappability_tracks.sh -------------------------------------------------------------------------------- /setup_scripts/install_processing_dependencies.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cboix/EPIMAP_ANALYSIS/HEAD/setup_scripts/install_processing_dependencies.sh -------------------------------------------------------------------------------- /setup_scripts/make_TSS_windows.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cboix/EPIMAP_ANALYSIS/HEAD/setup_scripts/make_TSS_windows.sh -------------------------------------------------------------------------------- /setup_scripts/make_enhstate_list.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cboix/EPIMAP_ANALYSIS/HEAD/setup_scripts/make_enhstate_list.sh -------------------------------------------------------------------------------- /setup_scripts/make_impobs_tables.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cboix/EPIMAP_ANALYSIS/HEAD/setup_scripts/make_impobs_tables.sh -------------------------------------------------------------------------------- /setup_scripts/make_uniform_control.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cboix/EPIMAP_ANALYSIS/HEAD/setup_scripts/make_uniform_control.sh -------------------------------------------------------------------------------- /tree_vis/server.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cboix/EPIMAP_ANALYSIS/HEAD/tree_vis/server.R -------------------------------------------------------------------------------- /tree_vis/ui.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cboix/EPIMAP_ANALYSIS/HEAD/tree_vis/ui.R -------------------------------------------------------------------------------- /utils/addRank2NarrowPeakFile.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cboix/EPIMAP_ANALYSIS/HEAD/utils/addRank2NarrowPeakFile.sh -------------------------------------------------------------------------------- /utils/aggregate_binary_txt_to_npy.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cboix/EPIMAP_ANALYSIS/HEAD/utils/aggregate_binary_txt_to_npy.py -------------------------------------------------------------------------------- /utils/bedgraph_compress.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cboix/EPIMAP_ANALYSIS/HEAD/utils/bedgraph_compress.sh -------------------------------------------------------------------------------- /utils/callpeak_from_imputedbw.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cboix/EPIMAP_ANALYSIS/HEAD/utils/callpeak_from_imputedbw.sh -------------------------------------------------------------------------------- /utils/catch_rerun.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cboix/EPIMAP_ANALYSIS/HEAD/utils/catch_rerun.sh -------------------------------------------------------------------------------- /utils/chunk_bed.awk: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cboix/EPIMAP_ANALYSIS/HEAD/utils/chunk_bed.awk -------------------------------------------------------------------------------- /utils/clean_cpdir.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cboix/EPIMAP_ANALYSIS/HEAD/utils/clean_cpdir.sh -------------------------------------------------------------------------------- /utils/cluster_binary_mat.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cboix/EPIMAP_ANALYSIS/HEAD/utils/cluster_binary_mat.py -------------------------------------------------------------------------------- /utils/compress_bw_to_hd5py.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cboix/EPIMAP_ANALYSIS/HEAD/utils/compress_bw_to_hd5py.py -------------------------------------------------------------------------------- /utils/convert_array_to_zarr.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cboix/EPIMAP_ANALYSIS/HEAD/utils/convert_array_to_zarr.py -------------------------------------------------------------------------------- /utils/convert_meme_motifs.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cboix/EPIMAP_ANALYSIS/HEAD/utils/convert_meme_motifs.py -------------------------------------------------------------------------------- /utils/convert_to_fixed_step_bed.awk: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cboix/EPIMAP_ANALYSIS/HEAD/utils/convert_to_fixed_step_bed.awk -------------------------------------------------------------------------------- /utils/create_chmm_state_possiblelist.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cboix/EPIMAP_ANALYSIS/HEAD/utils/create_chmm_state_possiblelist.py -------------------------------------------------------------------------------- /utils/extract_allbw_region.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cboix/EPIMAP_ANALYSIS/HEAD/utils/extract_allbw_region.sh -------------------------------------------------------------------------------- /utils/extract_bw_bins.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cboix/EPIMAP_ANALYSIS/HEAD/utils/extract_bw_bins.R -------------------------------------------------------------------------------- /utils/extract_bw_on_peaks.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cboix/EPIMAP_ANALYSIS/HEAD/utils/extract_bw_on_peaks.sh -------------------------------------------------------------------------------- /utils/extract_plot_chromHMM_region.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cboix/EPIMAP_ANALYSIS/HEAD/utils/extract_plot_chromHMM_region.sh -------------------------------------------------------------------------------- /utils/extract_signaldistr_statespecific.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cboix/EPIMAP_ANALYSIS/HEAD/utils/extract_signaldistr_statespecific.py -------------------------------------------------------------------------------- /utils/get_enh_prom_idx.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cboix/EPIMAP_ANALYSIS/HEAD/utils/get_enh_prom_idx.py -------------------------------------------------------------------------------- /utils/merge_hdf5_matrices.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cboix/EPIMAP_ANALYSIS/HEAD/utils/merge_hdf5_matrices.py -------------------------------------------------------------------------------- /utils/parse_config.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cboix/EPIMAP_ANALYSIS/HEAD/utils/parse_config.py -------------------------------------------------------------------------------- /utils/parse_config.pyc: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cboix/EPIMAP_ANALYSIS/HEAD/utils/parse_config.pyc -------------------------------------------------------------------------------- /utils/precompute_correlations.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cboix/EPIMAP_ANALYSIS/HEAD/utils/precompute_correlations.py -------------------------------------------------------------------------------- /utils/proc_mtx_to_sparse.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cboix/EPIMAP_ANALYSIS/HEAD/utils/proc_mtx_to_sparse.py -------------------------------------------------------------------------------- /utils/txtdf_to_sparse.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cboix/EPIMAP_ANALYSIS/HEAD/utils/txtdf_to_sparse.py --------------------------------------------------------------------------------