├── .gitattributes ├── .gitignore ├── CHANGELOG.md ├── CITATIONS.md ├── LICENCE.md ├── README.md ├── bin ├── .upload_to_figshare.sh ├── bamToBed_and_atacShift.sh ├── export_df_to_bed.R ├── functions_grouped_plot.R ├── functions_plot_volcano_PCA.R ├── functions_pvalue_plots.R ├── get_chrom_states_names_vec.R ├── get_formatted_table.R ├── get_merged_columns.R ├── get_new_name_by_unique_character.R ├── get_prom_bed_df_table.R ├── grepl_filter.R ├── plotBamCoverage.sh ├── plotPCAandCorMat.sh ├── plot_saturation_curve.R ├── plot_venn_diagrams.R ├── read_from_nextflow.R ├── splitMACS2SubPeaks.pl └── splitting_DAR_in_subsets_functions.R ├── case_study ├── 1__creating_the_case_study.sh ├── 2__running_the_case_study.sh ├── 3__getting_figure_panels.sh └── 4__making_figures.R ├── conf ├── .example.cactus.config ├── containers.config ├── reports.config ├── ressources.config ├── run_defaults.config ├── species.config └── version.config ├── docs ├── 1_Intro │ ├── Flowchart.md │ ├── NAISS.sh │ ├── Outputs_structure.md │ ├── Quick_start.md │ ├── installing_dependencies.sh │ ├── running_the_test_datasets.sh │ ├── troubleshooting.sh │ ├── tutorial.md │ └── tutorial.sh ├── 2_Install │ ├── 2_Install.md │ ├── Containers.md │ ├── Dependencies.md │ ├── References.md │ └── Test_datasets.md ├── 3_Inputs │ ├── 3_Inputs.md │ ├── Data.md │ ├── Design.md │ ├── Parameters.md │ └── all_config_entries.txt ├── 4_Prepro │ ├── 4_Prepro.md │ ├── ATAC_peaks.md │ ├── ATAC_reads.md │ └── mRNA.md ├── 5_DA │ ├── 5_DA.md │ ├── DA_ATAC.md │ ├── DA_mRNA.md │ └── Split.md ├── 6_Enrich │ ├── 6_Enrich.md │ ├── Enrichment.md │ ├── Figures.md │ └── Tables.md ├── examples │ ├── html │ │ ├── ATAC__multiQC.html │ │ └── mRNA__multiQC.html │ ├── png │ │ ├── ATAC__all__1000__all__CHIP__heatmap.png │ │ ├── ATAC__all__1000__all__chrom_states__heatmap.png │ │ ├── ATAC__all__1000__all__func_anno_BP__heatmap.png │ │ ├── ATAC__all__1000__all__func_anno_KEGG__heatmap.png │ │ ├── ATAC__all__1000__all__genes_self__heatmap.png │ │ ├── ATAC__all__1000__all__motifs__heatmap.png │ │ ├── ATAC__all__1000__all__peaks_self__heatmap.png │ │ ├── ATAC__all__1000__ctl__func_anno_KEGG__heatmap.png │ │ ├── ATAC__all__1000__ctl__genes_self__heatmap.png │ │ ├── ATAC__all__down__1000__hmg4_vs_ctl__CHIP__barplot.png │ │ ├── ATAC__all__down__1000__hmg4_vs_ctl__chrom_states__barplot.png │ │ ├── ATAC__all__down__1000__hmg4_vs_ctl__func_anno_BP__barplot.png │ │ ├── ATAC__all__down__1000__hmg4_vs_ctl__func_anno_KEGG__barplot.png │ │ ├── ATAC__all__down__1000__hmg4_vs_ctl__genes_self__barplot.png │ │ ├── ATAC__all__down__1000__hmg4_vs_ctl__peaks_self__barplot.png │ │ ├── ATAC__all__down__1000__hmg4_vs_spt16__motifs__barplot.png │ │ ├── ATAC__peaks__grouped__annotation_barplot.png │ │ ├── ATAC__peaks__grouped__average_profile.png │ │ ├── ATAC__peaks__grouped__distance_to_TSS.png │ │ ├── all__1000__hmg4_vs_ctl__venn_up_and_down.png │ │ ├── all__down__1000__hmg4_vs_ctl__venn_up_or_down.png │ │ ├── all__up__1000__hmg4_vs_ctl__venn_up_or_down.png │ │ ├── both__all__1000__ctl__func_anno_KEGG__heatmap.png │ │ ├── both__all__1000__ctl__genes_self__heatmap.png │ │ ├── ctl_1__average_profile.png │ │ ├── ctl_1__insert_size.png │ │ ├── ctl_1__peaks_coverage.png │ │ ├── ctl_1__reads_coverage.png │ │ ├── ctl_1__saturation_curve.png │ │ ├── hmg4_3__saturation_curve.png │ │ ├── hmg4_vs_ctl__ATAC_FDR_by_PA.png │ │ ├── hmg4_vs_ctl__ATAC_PCA_1_2.png │ │ ├── hmg4_vs_ctl__ATAC_PCA_3_4.png │ │ ├── hmg4_vs_ctl__ATAC_other_plots-1.png │ │ ├── hmg4_vs_ctl__ATAC_other_plots-2.png │ │ ├── hmg4_vs_ctl__ATAC_other_plots-3.png │ │ ├── hmg4_vs_ctl__ATAC_other_plots.png │ │ ├── hmg4_vs_ctl__ATAC_volcano.png │ │ ├── hmg4_vs_ctl__mRNA_PCA_1_2.png │ │ ├── hmg4_vs_ctl__mRNA_PCA_3_4.png │ │ ├── hmg4_vs_ctl__mRNA_other_plots-1.png │ │ ├── hmg4_vs_ctl__mRNA_other_plots-2.png │ │ ├── hmg4_vs_ctl__mRNA_other_plots.png │ │ ├── hmg4_vs_ctl__mRNA_volcano.png │ │ ├── hmg4_vs_spt16__ATAC_volcano.png │ │ ├── hmg4_vs_spt16__ATAC_volcano__no_rtr.png │ │ ├── mRNA__Null__1000__ctl__func_anno_KEGG__heatmap.png │ │ ├── mRNA__Null__1000__ctl__genes_self__heatmap.png │ │ ├── mRNA_volcano__no_gtr.png │ │ ├── mRNA_volcano__with_gtr.png │ │ ├── pca_top5000_without_control_pca.png │ │ └── spearman_correlation_heatmap_without_outliers_without_control_cor.png │ └── xlsx_png │ │ ├── ATAC_detailled_1.png │ │ ├── ATAC_detailled_2.png │ │ ├── ATAC_detailled_3.png │ │ ├── CHIP.png │ │ ├── both__all__1000__ctl__KEGG__table.png │ │ ├── chrom_states.png │ │ ├── func_anno__BP.png │ │ ├── func_anno__KEGG.png │ │ ├── genes_self.png │ │ ├── mRNA_detailled_1.png │ │ ├── mRNA_detailled_2.png │ │ ├── motifs.png │ │ ├── peaks_self.png │ │ ├── res_filter.png │ │ └── res_simple.png ├── images │ ├── cactus_all_steps.png │ ├── cactus_all_steps.svg │ ├── dag.html │ ├── dag.svg │ ├── dag_get_data.svg │ ├── dag_get_data__vertical.svg │ ├── figure_1.png │ ├── logo_cactus.png │ ├── splitting.png │ └── splitting_filters.png ├── index.html ├── menu │ ├── add_menu.sh │ └── menu.md └── util │ ├── containers │ ├── containers_info.tsv │ ├── containers_info_galaxy.tsv │ ├── containers_info_not_galaxy.tsv │ ├── containers_info_size.tsv │ └── containers_info_size_1.tsv │ ├── get_all_parameters.sh │ └── get_figure_examples.sh ├── figshare ├── bin │ └── creating_archive_and_uploading_them_to_figshare.sh └── metadata │ ├── README.txt │ └── manifest.txt ├── main.nf ├── nextflow.config ├── scripts ├── create_references │ ├── bin │ │ ├── check_checksum_ensembl.sh │ │ ├── encode_chip_functions.R │ │ ├── get_blacklisted_ensembl_file.sh │ │ ├── get_fasta_and_gff.sh │ │ ├── get_linebreak.R │ │ ├── get_tab.R │ │ ├── get_tab.sh │ │ ├── make_chip_ontology_groups_functions.R │ │ └── make_timestamp.R │ ├── conf │ │ ├── containers.config │ │ └── reports.config │ ├── create_references.nf │ └── nextflow.config ├── create_test_datasets │ ├── bin │ │ ├── 0__initialization.sh │ │ ├── 1__get_fastq.sh │ │ ├── 2__subsample_reads.sh │ │ ├── 3__make_design_files__fly.sh │ │ ├── 3__make_design_files__human.sh │ │ ├── 3__make_design_files__mouse.sh │ │ ├── 3__make_design_files__worm.sh │ │ ├── create_test_datasets_functions.sh │ │ ├── make_application_note_dirs.sh │ │ ├── nextflow.config │ │ └── subsample_reads.nf │ ├── create_test_datasets.sh │ ├── datasets_details.plain │ └── samples_ids │ │ ├── gsm_accession │ │ ├── gsm_fly.txt │ │ ├── gsm_human.txt │ │ ├── gsm_mouse.txt │ │ ├── gsm_mouse__details.txt │ │ ├── gsm_test.txt │ │ ├── gsm_worm.txt │ │ └── gsm_worm_case_study.txt │ │ ├── preprocessing │ │ └── report │ │ │ └── genome_and_transcriptome_size.txt │ │ └── srr_accession │ │ ├── srr_fly.txt │ │ ├── srr_human.txt │ │ ├── srr_mouse.txt │ │ ├── srr_test.txt │ │ ├── srr_worm.txt │ │ └── srr_worm_case_study.txt └── download │ ├── download.nf │ ├── files.config │ └── nextflow.config └── test_datasets ├── fly ├── design │ ├── atac_fastq.tsv │ ├── comparisons.tsv │ ├── genes_to_remove.tsv │ ├── genes_to_remove_empty.tsv │ ├── groups.tsv │ ├── mrna_fastq.tsv │ └── regions_to_remove.tsv └── parameters │ ├── full_test.yml │ ├── no_enrich.yml │ └── no_enrich__no_gtr.yml ├── human ├── design │ ├── atac_fastq.tsv │ ├── comparisons.tsv │ ├── genes_to_remove.tsv │ ├── groups.tsv │ ├── mrna_fastq.tsv │ └── regions_to_remove.tsv └── parameters │ ├── full_test.yml │ └── no_enrich.yml ├── mouse ├── design │ ├── atac_fastq.tsv │ ├── comparisons.tsv │ ├── genes_to_remove.tsv │ ├── groups.tsv │ ├── mrna_fastq.tsv │ └── regions_to_remove.tsv └── parameters │ ├── full_test.yml │ └── no_enrich.yml ├── running_the_case_study.sh ├── running_the_test_datasets.sh └── worm ├── design ├── atac_fastq.tsv ├── atac_fastq__with_input.tsv ├── atac_fastq__without_input.tsv ├── comparisons.tsv ├── genes_to_remove.tsv ├── groups.tsv ├── mrna_fastq.tsv ├── regions_to_remove.tsv └── regions_to_remove_empty.tsv └── parameters ├── enrich_only_chip.yml ├── enrich_only_genes_self.yml ├── enrich_only_genes_self__FDR.yml ├── full_test.yml ├── no_enrich.yml └── no_enrich__no_rtr.yml /.gitattributes: -------------------------------------------------------------------------------- 1 | *.config linguist-language=nextflow -------------------------------------------------------------------------------- /.gitignore: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jsalignon/cactus/HEAD/.gitignore -------------------------------------------------------------------------------- /CHANGELOG.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jsalignon/cactus/HEAD/CHANGELOG.md -------------------------------------------------------------------------------- /CITATIONS.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jsalignon/cactus/HEAD/CITATIONS.md -------------------------------------------------------------------------------- /LICENCE.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jsalignon/cactus/HEAD/LICENCE.md -------------------------------------------------------------------------------- /README.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jsalignon/cactus/HEAD/README.md -------------------------------------------------------------------------------- /bin/.upload_to_figshare.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jsalignon/cactus/HEAD/bin/.upload_to_figshare.sh -------------------------------------------------------------------------------- /bin/bamToBed_and_atacShift.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jsalignon/cactus/HEAD/bin/bamToBed_and_atacShift.sh -------------------------------------------------------------------------------- /bin/export_df_to_bed.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jsalignon/cactus/HEAD/bin/export_df_to_bed.R -------------------------------------------------------------------------------- /bin/functions_grouped_plot.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jsalignon/cactus/HEAD/bin/functions_grouped_plot.R -------------------------------------------------------------------------------- /bin/functions_plot_volcano_PCA.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jsalignon/cactus/HEAD/bin/functions_plot_volcano_PCA.R -------------------------------------------------------------------------------- /bin/functions_pvalue_plots.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jsalignon/cactus/HEAD/bin/functions_pvalue_plots.R -------------------------------------------------------------------------------- /bin/get_chrom_states_names_vec.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jsalignon/cactus/HEAD/bin/get_chrom_states_names_vec.R -------------------------------------------------------------------------------- /bin/get_formatted_table.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jsalignon/cactus/HEAD/bin/get_formatted_table.R -------------------------------------------------------------------------------- /bin/get_merged_columns.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jsalignon/cactus/HEAD/bin/get_merged_columns.R -------------------------------------------------------------------------------- /bin/get_new_name_by_unique_character.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jsalignon/cactus/HEAD/bin/get_new_name_by_unique_character.R -------------------------------------------------------------------------------- /bin/get_prom_bed_df_table.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jsalignon/cactus/HEAD/bin/get_prom_bed_df_table.R -------------------------------------------------------------------------------- /bin/grepl_filter.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jsalignon/cactus/HEAD/bin/grepl_filter.R -------------------------------------------------------------------------------- /bin/plotBamCoverage.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jsalignon/cactus/HEAD/bin/plotBamCoverage.sh -------------------------------------------------------------------------------- /bin/plotPCAandCorMat.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jsalignon/cactus/HEAD/bin/plotPCAandCorMat.sh -------------------------------------------------------------------------------- /bin/plot_saturation_curve.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jsalignon/cactus/HEAD/bin/plot_saturation_curve.R -------------------------------------------------------------------------------- /bin/plot_venn_diagrams.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jsalignon/cactus/HEAD/bin/plot_venn_diagrams.R -------------------------------------------------------------------------------- /bin/read_from_nextflow.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jsalignon/cactus/HEAD/bin/read_from_nextflow.R -------------------------------------------------------------------------------- /bin/splitMACS2SubPeaks.pl: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jsalignon/cactus/HEAD/bin/splitMACS2SubPeaks.pl -------------------------------------------------------------------------------- /bin/splitting_DAR_in_subsets_functions.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jsalignon/cactus/HEAD/bin/splitting_DAR_in_subsets_functions.R -------------------------------------------------------------------------------- /case_study/1__creating_the_case_study.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jsalignon/cactus/HEAD/case_study/1__creating_the_case_study.sh -------------------------------------------------------------------------------- /case_study/2__running_the_case_study.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jsalignon/cactus/HEAD/case_study/2__running_the_case_study.sh -------------------------------------------------------------------------------- /case_study/3__getting_figure_panels.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jsalignon/cactus/HEAD/case_study/3__getting_figure_panels.sh -------------------------------------------------------------------------------- /case_study/4__making_figures.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jsalignon/cactus/HEAD/case_study/4__making_figures.R -------------------------------------------------------------------------------- /conf/.example.cactus.config: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jsalignon/cactus/HEAD/conf/.example.cactus.config -------------------------------------------------------------------------------- /conf/containers.config: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jsalignon/cactus/HEAD/conf/containers.config -------------------------------------------------------------------------------- /conf/reports.config: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jsalignon/cactus/HEAD/conf/reports.config -------------------------------------------------------------------------------- /conf/ressources.config: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jsalignon/cactus/HEAD/conf/ressources.config -------------------------------------------------------------------------------- /conf/run_defaults.config: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jsalignon/cactus/HEAD/conf/run_defaults.config -------------------------------------------------------------------------------- /conf/species.config: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jsalignon/cactus/HEAD/conf/species.config -------------------------------------------------------------------------------- /conf/version.config: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jsalignon/cactus/HEAD/conf/version.config -------------------------------------------------------------------------------- /docs/1_Intro/Flowchart.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jsalignon/cactus/HEAD/docs/1_Intro/Flowchart.md -------------------------------------------------------------------------------- /docs/1_Intro/NAISS.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jsalignon/cactus/HEAD/docs/1_Intro/NAISS.sh -------------------------------------------------------------------------------- /docs/1_Intro/Outputs_structure.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jsalignon/cactus/HEAD/docs/1_Intro/Outputs_structure.md -------------------------------------------------------------------------------- /docs/1_Intro/Quick_start.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jsalignon/cactus/HEAD/docs/1_Intro/Quick_start.md -------------------------------------------------------------------------------- /docs/1_Intro/installing_dependencies.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jsalignon/cactus/HEAD/docs/1_Intro/installing_dependencies.sh -------------------------------------------------------------------------------- /docs/1_Intro/running_the_test_datasets.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jsalignon/cactus/HEAD/docs/1_Intro/running_the_test_datasets.sh -------------------------------------------------------------------------------- /docs/1_Intro/troubleshooting.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jsalignon/cactus/HEAD/docs/1_Intro/troubleshooting.sh -------------------------------------------------------------------------------- /docs/1_Intro/tutorial.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jsalignon/cactus/HEAD/docs/1_Intro/tutorial.md -------------------------------------------------------------------------------- /docs/1_Intro/tutorial.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jsalignon/cactus/HEAD/docs/1_Intro/tutorial.sh -------------------------------------------------------------------------------- /docs/2_Install/2_Install.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jsalignon/cactus/HEAD/docs/2_Install/2_Install.md -------------------------------------------------------------------------------- /docs/2_Install/Containers.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jsalignon/cactus/HEAD/docs/2_Install/Containers.md -------------------------------------------------------------------------------- /docs/2_Install/Dependencies.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jsalignon/cactus/HEAD/docs/2_Install/Dependencies.md -------------------------------------------------------------------------------- /docs/2_Install/References.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jsalignon/cactus/HEAD/docs/2_Install/References.md -------------------------------------------------------------------------------- /docs/2_Install/Test_datasets.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jsalignon/cactus/HEAD/docs/2_Install/Test_datasets.md -------------------------------------------------------------------------------- /docs/3_Inputs/3_Inputs.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jsalignon/cactus/HEAD/docs/3_Inputs/3_Inputs.md -------------------------------------------------------------------------------- /docs/3_Inputs/Data.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jsalignon/cactus/HEAD/docs/3_Inputs/Data.md -------------------------------------------------------------------------------- /docs/3_Inputs/Design.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jsalignon/cactus/HEAD/docs/3_Inputs/Design.md -------------------------------------------------------------------------------- /docs/3_Inputs/Parameters.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jsalignon/cactus/HEAD/docs/3_Inputs/Parameters.md -------------------------------------------------------------------------------- /docs/3_Inputs/all_config_entries.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jsalignon/cactus/HEAD/docs/3_Inputs/all_config_entries.txt -------------------------------------------------------------------------------- /docs/4_Prepro/4_Prepro.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jsalignon/cactus/HEAD/docs/4_Prepro/4_Prepro.md -------------------------------------------------------------------------------- /docs/4_Prepro/ATAC_peaks.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jsalignon/cactus/HEAD/docs/4_Prepro/ATAC_peaks.md -------------------------------------------------------------------------------- /docs/4_Prepro/ATAC_reads.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jsalignon/cactus/HEAD/docs/4_Prepro/ATAC_reads.md -------------------------------------------------------------------------------- /docs/4_Prepro/mRNA.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jsalignon/cactus/HEAD/docs/4_Prepro/mRNA.md -------------------------------------------------------------------------------- /docs/5_DA/5_DA.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jsalignon/cactus/HEAD/docs/5_DA/5_DA.md -------------------------------------------------------------------------------- /docs/5_DA/DA_ATAC.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jsalignon/cactus/HEAD/docs/5_DA/DA_ATAC.md -------------------------------------------------------------------------------- /docs/5_DA/DA_mRNA.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jsalignon/cactus/HEAD/docs/5_DA/DA_mRNA.md -------------------------------------------------------------------------------- /docs/5_DA/Split.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jsalignon/cactus/HEAD/docs/5_DA/Split.md -------------------------------------------------------------------------------- /docs/6_Enrich/6_Enrich.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jsalignon/cactus/HEAD/docs/6_Enrich/6_Enrich.md -------------------------------------------------------------------------------- /docs/6_Enrich/Enrichment.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jsalignon/cactus/HEAD/docs/6_Enrich/Enrichment.md -------------------------------------------------------------------------------- /docs/6_Enrich/Figures.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jsalignon/cactus/HEAD/docs/6_Enrich/Figures.md -------------------------------------------------------------------------------- /docs/6_Enrich/Tables.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jsalignon/cactus/HEAD/docs/6_Enrich/Tables.md -------------------------------------------------------------------------------- /docs/examples/html/ATAC__multiQC.html: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jsalignon/cactus/HEAD/docs/examples/html/ATAC__multiQC.html -------------------------------------------------------------------------------- /docs/examples/html/mRNA__multiQC.html: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jsalignon/cactus/HEAD/docs/examples/html/mRNA__multiQC.html -------------------------------------------------------------------------------- /docs/examples/png/ATAC__all__1000__all__CHIP__heatmap.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jsalignon/cactus/HEAD/docs/examples/png/ATAC__all__1000__all__CHIP__heatmap.png -------------------------------------------------------------------------------- /docs/examples/png/ATAC__all__1000__all__chrom_states__heatmap.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jsalignon/cactus/HEAD/docs/examples/png/ATAC__all__1000__all__chrom_states__heatmap.png -------------------------------------------------------------------------------- /docs/examples/png/ATAC__all__1000__all__func_anno_BP__heatmap.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jsalignon/cactus/HEAD/docs/examples/png/ATAC__all__1000__all__func_anno_BP__heatmap.png -------------------------------------------------------------------------------- /docs/examples/png/ATAC__all__1000__all__func_anno_KEGG__heatmap.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jsalignon/cactus/HEAD/docs/examples/png/ATAC__all__1000__all__func_anno_KEGG__heatmap.png -------------------------------------------------------------------------------- /docs/examples/png/ATAC__all__1000__all__genes_self__heatmap.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jsalignon/cactus/HEAD/docs/examples/png/ATAC__all__1000__all__genes_self__heatmap.png -------------------------------------------------------------------------------- /docs/examples/png/ATAC__all__1000__all__motifs__heatmap.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jsalignon/cactus/HEAD/docs/examples/png/ATAC__all__1000__all__motifs__heatmap.png -------------------------------------------------------------------------------- /docs/examples/png/ATAC__all__1000__all__peaks_self__heatmap.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jsalignon/cactus/HEAD/docs/examples/png/ATAC__all__1000__all__peaks_self__heatmap.png -------------------------------------------------------------------------------- /docs/examples/png/ATAC__all__1000__ctl__func_anno_KEGG__heatmap.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jsalignon/cactus/HEAD/docs/examples/png/ATAC__all__1000__ctl__func_anno_KEGG__heatmap.png -------------------------------------------------------------------------------- /docs/examples/png/ATAC__all__1000__ctl__genes_self__heatmap.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jsalignon/cactus/HEAD/docs/examples/png/ATAC__all__1000__ctl__genes_self__heatmap.png -------------------------------------------------------------------------------- /docs/examples/png/ATAC__all__down__1000__hmg4_vs_ctl__CHIP__barplot.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jsalignon/cactus/HEAD/docs/examples/png/ATAC__all__down__1000__hmg4_vs_ctl__CHIP__barplot.png -------------------------------------------------------------------------------- /docs/examples/png/ATAC__all__down__1000__hmg4_vs_ctl__chrom_states__barplot.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jsalignon/cactus/HEAD/docs/examples/png/ATAC__all__down__1000__hmg4_vs_ctl__chrom_states__barplot.png -------------------------------------------------------------------------------- /docs/examples/png/ATAC__all__down__1000__hmg4_vs_ctl__func_anno_BP__barplot.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jsalignon/cactus/HEAD/docs/examples/png/ATAC__all__down__1000__hmg4_vs_ctl__func_anno_BP__barplot.png -------------------------------------------------------------------------------- /docs/examples/png/ATAC__all__down__1000__hmg4_vs_ctl__func_anno_KEGG__barplot.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jsalignon/cactus/HEAD/docs/examples/png/ATAC__all__down__1000__hmg4_vs_ctl__func_anno_KEGG__barplot.png -------------------------------------------------------------------------------- /docs/examples/png/ATAC__all__down__1000__hmg4_vs_ctl__genes_self__barplot.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jsalignon/cactus/HEAD/docs/examples/png/ATAC__all__down__1000__hmg4_vs_ctl__genes_self__barplot.png -------------------------------------------------------------------------------- /docs/examples/png/ATAC__all__down__1000__hmg4_vs_ctl__peaks_self__barplot.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jsalignon/cactus/HEAD/docs/examples/png/ATAC__all__down__1000__hmg4_vs_ctl__peaks_self__barplot.png -------------------------------------------------------------------------------- /docs/examples/png/ATAC__all__down__1000__hmg4_vs_spt16__motifs__barplot.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jsalignon/cactus/HEAD/docs/examples/png/ATAC__all__down__1000__hmg4_vs_spt16__motifs__barplot.png -------------------------------------------------------------------------------- /docs/examples/png/ATAC__peaks__grouped__annotation_barplot.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jsalignon/cactus/HEAD/docs/examples/png/ATAC__peaks__grouped__annotation_barplot.png -------------------------------------------------------------------------------- /docs/examples/png/ATAC__peaks__grouped__average_profile.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jsalignon/cactus/HEAD/docs/examples/png/ATAC__peaks__grouped__average_profile.png -------------------------------------------------------------------------------- /docs/examples/png/ATAC__peaks__grouped__distance_to_TSS.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jsalignon/cactus/HEAD/docs/examples/png/ATAC__peaks__grouped__distance_to_TSS.png -------------------------------------------------------------------------------- /docs/examples/png/all__1000__hmg4_vs_ctl__venn_up_and_down.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jsalignon/cactus/HEAD/docs/examples/png/all__1000__hmg4_vs_ctl__venn_up_and_down.png -------------------------------------------------------------------------------- /docs/examples/png/all__down__1000__hmg4_vs_ctl__venn_up_or_down.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jsalignon/cactus/HEAD/docs/examples/png/all__down__1000__hmg4_vs_ctl__venn_up_or_down.png -------------------------------------------------------------------------------- /docs/examples/png/all__up__1000__hmg4_vs_ctl__venn_up_or_down.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jsalignon/cactus/HEAD/docs/examples/png/all__up__1000__hmg4_vs_ctl__venn_up_or_down.png -------------------------------------------------------------------------------- /docs/examples/png/both__all__1000__ctl__func_anno_KEGG__heatmap.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jsalignon/cactus/HEAD/docs/examples/png/both__all__1000__ctl__func_anno_KEGG__heatmap.png -------------------------------------------------------------------------------- /docs/examples/png/both__all__1000__ctl__genes_self__heatmap.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jsalignon/cactus/HEAD/docs/examples/png/both__all__1000__ctl__genes_self__heatmap.png -------------------------------------------------------------------------------- /docs/examples/png/ctl_1__average_profile.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jsalignon/cactus/HEAD/docs/examples/png/ctl_1__average_profile.png -------------------------------------------------------------------------------- /docs/examples/png/ctl_1__insert_size.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jsalignon/cactus/HEAD/docs/examples/png/ctl_1__insert_size.png -------------------------------------------------------------------------------- /docs/examples/png/ctl_1__peaks_coverage.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jsalignon/cactus/HEAD/docs/examples/png/ctl_1__peaks_coverage.png -------------------------------------------------------------------------------- /docs/examples/png/ctl_1__reads_coverage.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jsalignon/cactus/HEAD/docs/examples/png/ctl_1__reads_coverage.png -------------------------------------------------------------------------------- /docs/examples/png/ctl_1__saturation_curve.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jsalignon/cactus/HEAD/docs/examples/png/ctl_1__saturation_curve.png -------------------------------------------------------------------------------- /docs/examples/png/hmg4_3__saturation_curve.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jsalignon/cactus/HEAD/docs/examples/png/hmg4_3__saturation_curve.png -------------------------------------------------------------------------------- /docs/examples/png/hmg4_vs_ctl__ATAC_FDR_by_PA.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jsalignon/cactus/HEAD/docs/examples/png/hmg4_vs_ctl__ATAC_FDR_by_PA.png -------------------------------------------------------------------------------- /docs/examples/png/hmg4_vs_ctl__ATAC_PCA_1_2.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jsalignon/cactus/HEAD/docs/examples/png/hmg4_vs_ctl__ATAC_PCA_1_2.png -------------------------------------------------------------------------------- /docs/examples/png/hmg4_vs_ctl__ATAC_PCA_3_4.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jsalignon/cactus/HEAD/docs/examples/png/hmg4_vs_ctl__ATAC_PCA_3_4.png -------------------------------------------------------------------------------- /docs/examples/png/hmg4_vs_ctl__ATAC_other_plots-1.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jsalignon/cactus/HEAD/docs/examples/png/hmg4_vs_ctl__ATAC_other_plots-1.png -------------------------------------------------------------------------------- /docs/examples/png/hmg4_vs_ctl__ATAC_other_plots-2.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jsalignon/cactus/HEAD/docs/examples/png/hmg4_vs_ctl__ATAC_other_plots-2.png -------------------------------------------------------------------------------- /docs/examples/png/hmg4_vs_ctl__ATAC_other_plots-3.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jsalignon/cactus/HEAD/docs/examples/png/hmg4_vs_ctl__ATAC_other_plots-3.png -------------------------------------------------------------------------------- /docs/examples/png/hmg4_vs_ctl__ATAC_other_plots.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jsalignon/cactus/HEAD/docs/examples/png/hmg4_vs_ctl__ATAC_other_plots.png -------------------------------------------------------------------------------- /docs/examples/png/hmg4_vs_ctl__ATAC_volcano.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jsalignon/cactus/HEAD/docs/examples/png/hmg4_vs_ctl__ATAC_volcano.png -------------------------------------------------------------------------------- /docs/examples/png/hmg4_vs_ctl__mRNA_PCA_1_2.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jsalignon/cactus/HEAD/docs/examples/png/hmg4_vs_ctl__mRNA_PCA_1_2.png -------------------------------------------------------------------------------- /docs/examples/png/hmg4_vs_ctl__mRNA_PCA_3_4.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jsalignon/cactus/HEAD/docs/examples/png/hmg4_vs_ctl__mRNA_PCA_3_4.png -------------------------------------------------------------------------------- /docs/examples/png/hmg4_vs_ctl__mRNA_other_plots-1.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jsalignon/cactus/HEAD/docs/examples/png/hmg4_vs_ctl__mRNA_other_plots-1.png -------------------------------------------------------------------------------- /docs/examples/png/hmg4_vs_ctl__mRNA_other_plots-2.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jsalignon/cactus/HEAD/docs/examples/png/hmg4_vs_ctl__mRNA_other_plots-2.png -------------------------------------------------------------------------------- /docs/examples/png/hmg4_vs_ctl__mRNA_other_plots.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jsalignon/cactus/HEAD/docs/examples/png/hmg4_vs_ctl__mRNA_other_plots.png -------------------------------------------------------------------------------- /docs/examples/png/hmg4_vs_ctl__mRNA_volcano.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jsalignon/cactus/HEAD/docs/examples/png/hmg4_vs_ctl__mRNA_volcano.png -------------------------------------------------------------------------------- /docs/examples/png/hmg4_vs_spt16__ATAC_volcano.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jsalignon/cactus/HEAD/docs/examples/png/hmg4_vs_spt16__ATAC_volcano.png -------------------------------------------------------------------------------- /docs/examples/png/hmg4_vs_spt16__ATAC_volcano__no_rtr.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jsalignon/cactus/HEAD/docs/examples/png/hmg4_vs_spt16__ATAC_volcano__no_rtr.png -------------------------------------------------------------------------------- /docs/examples/png/mRNA__Null__1000__ctl__func_anno_KEGG__heatmap.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jsalignon/cactus/HEAD/docs/examples/png/mRNA__Null__1000__ctl__func_anno_KEGG__heatmap.png -------------------------------------------------------------------------------- /docs/examples/png/mRNA__Null__1000__ctl__genes_self__heatmap.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jsalignon/cactus/HEAD/docs/examples/png/mRNA__Null__1000__ctl__genes_self__heatmap.png -------------------------------------------------------------------------------- /docs/examples/png/mRNA_volcano__no_gtr.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jsalignon/cactus/HEAD/docs/examples/png/mRNA_volcano__no_gtr.png -------------------------------------------------------------------------------- /docs/examples/png/mRNA_volcano__with_gtr.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jsalignon/cactus/HEAD/docs/examples/png/mRNA_volcano__with_gtr.png -------------------------------------------------------------------------------- /docs/examples/png/pca_top5000_without_control_pca.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jsalignon/cactus/HEAD/docs/examples/png/pca_top5000_without_control_pca.png -------------------------------------------------------------------------------- /docs/examples/png/spearman_correlation_heatmap_without_outliers_without_control_cor.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jsalignon/cactus/HEAD/docs/examples/png/spearman_correlation_heatmap_without_outliers_without_control_cor.png -------------------------------------------------------------------------------- /docs/examples/xlsx_png/ATAC_detailled_1.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jsalignon/cactus/HEAD/docs/examples/xlsx_png/ATAC_detailled_1.png -------------------------------------------------------------------------------- /docs/examples/xlsx_png/ATAC_detailled_2.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jsalignon/cactus/HEAD/docs/examples/xlsx_png/ATAC_detailled_2.png -------------------------------------------------------------------------------- /docs/examples/xlsx_png/ATAC_detailled_3.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jsalignon/cactus/HEAD/docs/examples/xlsx_png/ATAC_detailled_3.png -------------------------------------------------------------------------------- /docs/examples/xlsx_png/CHIP.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jsalignon/cactus/HEAD/docs/examples/xlsx_png/CHIP.png -------------------------------------------------------------------------------- /docs/examples/xlsx_png/both__all__1000__ctl__KEGG__table.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jsalignon/cactus/HEAD/docs/examples/xlsx_png/both__all__1000__ctl__KEGG__table.png -------------------------------------------------------------------------------- /docs/examples/xlsx_png/chrom_states.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jsalignon/cactus/HEAD/docs/examples/xlsx_png/chrom_states.png -------------------------------------------------------------------------------- /docs/examples/xlsx_png/func_anno__BP.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jsalignon/cactus/HEAD/docs/examples/xlsx_png/func_anno__BP.png -------------------------------------------------------------------------------- /docs/examples/xlsx_png/func_anno__KEGG.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jsalignon/cactus/HEAD/docs/examples/xlsx_png/func_anno__KEGG.png -------------------------------------------------------------------------------- /docs/examples/xlsx_png/genes_self.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jsalignon/cactus/HEAD/docs/examples/xlsx_png/genes_self.png -------------------------------------------------------------------------------- /docs/examples/xlsx_png/mRNA_detailled_1.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jsalignon/cactus/HEAD/docs/examples/xlsx_png/mRNA_detailled_1.png -------------------------------------------------------------------------------- /docs/examples/xlsx_png/mRNA_detailled_2.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jsalignon/cactus/HEAD/docs/examples/xlsx_png/mRNA_detailled_2.png -------------------------------------------------------------------------------- /docs/examples/xlsx_png/motifs.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jsalignon/cactus/HEAD/docs/examples/xlsx_png/motifs.png -------------------------------------------------------------------------------- /docs/examples/xlsx_png/peaks_self.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jsalignon/cactus/HEAD/docs/examples/xlsx_png/peaks_self.png -------------------------------------------------------------------------------- /docs/examples/xlsx_png/res_filter.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jsalignon/cactus/HEAD/docs/examples/xlsx_png/res_filter.png -------------------------------------------------------------------------------- /docs/examples/xlsx_png/res_simple.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jsalignon/cactus/HEAD/docs/examples/xlsx_png/res_simple.png -------------------------------------------------------------------------------- /docs/images/cactus_all_steps.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jsalignon/cactus/HEAD/docs/images/cactus_all_steps.png -------------------------------------------------------------------------------- /docs/images/cactus_all_steps.svg: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jsalignon/cactus/HEAD/docs/images/cactus_all_steps.svg -------------------------------------------------------------------------------- /docs/images/dag.html: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jsalignon/cactus/HEAD/docs/images/dag.html -------------------------------------------------------------------------------- /docs/images/dag.svg: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jsalignon/cactus/HEAD/docs/images/dag.svg -------------------------------------------------------------------------------- /docs/images/dag_get_data.svg: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jsalignon/cactus/HEAD/docs/images/dag_get_data.svg -------------------------------------------------------------------------------- /docs/images/dag_get_data__vertical.svg: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jsalignon/cactus/HEAD/docs/images/dag_get_data__vertical.svg -------------------------------------------------------------------------------- /docs/images/figure_1.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jsalignon/cactus/HEAD/docs/images/figure_1.png -------------------------------------------------------------------------------- /docs/images/logo_cactus.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jsalignon/cactus/HEAD/docs/images/logo_cactus.png -------------------------------------------------------------------------------- /docs/images/splitting.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jsalignon/cactus/HEAD/docs/images/splitting.png -------------------------------------------------------------------------------- /docs/images/splitting_filters.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jsalignon/cactus/HEAD/docs/images/splitting_filters.png -------------------------------------------------------------------------------- /docs/index.html: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jsalignon/cactus/HEAD/docs/index.html -------------------------------------------------------------------------------- /docs/menu/add_menu.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jsalignon/cactus/HEAD/docs/menu/add_menu.sh -------------------------------------------------------------------------------- /docs/menu/menu.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jsalignon/cactus/HEAD/docs/menu/menu.md -------------------------------------------------------------------------------- /docs/util/containers/containers_info.tsv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jsalignon/cactus/HEAD/docs/util/containers/containers_info.tsv -------------------------------------------------------------------------------- /docs/util/containers/containers_info_galaxy.tsv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jsalignon/cactus/HEAD/docs/util/containers/containers_info_galaxy.tsv -------------------------------------------------------------------------------- /docs/util/containers/containers_info_not_galaxy.tsv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jsalignon/cactus/HEAD/docs/util/containers/containers_info_not_galaxy.tsv -------------------------------------------------------------------------------- /docs/util/containers/containers_info_size.tsv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jsalignon/cactus/HEAD/docs/util/containers/containers_info_size.tsv -------------------------------------------------------------------------------- /docs/util/containers/containers_info_size_1.tsv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jsalignon/cactus/HEAD/docs/util/containers/containers_info_size_1.tsv -------------------------------------------------------------------------------- /docs/util/get_all_parameters.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jsalignon/cactus/HEAD/docs/util/get_all_parameters.sh -------------------------------------------------------------------------------- /docs/util/get_figure_examples.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jsalignon/cactus/HEAD/docs/util/get_figure_examples.sh -------------------------------------------------------------------------------- /figshare/bin/creating_archive_and_uploading_them_to_figshare.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jsalignon/cactus/HEAD/figshare/bin/creating_archive_and_uploading_them_to_figshare.sh -------------------------------------------------------------------------------- /figshare/metadata/README.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jsalignon/cactus/HEAD/figshare/metadata/README.txt -------------------------------------------------------------------------------- /figshare/metadata/manifest.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jsalignon/cactus/HEAD/figshare/metadata/manifest.txt -------------------------------------------------------------------------------- /main.nf: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jsalignon/cactus/HEAD/main.nf -------------------------------------------------------------------------------- /nextflow.config: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jsalignon/cactus/HEAD/nextflow.config -------------------------------------------------------------------------------- /scripts/create_references/bin/check_checksum_ensembl.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jsalignon/cactus/HEAD/scripts/create_references/bin/check_checksum_ensembl.sh -------------------------------------------------------------------------------- /scripts/create_references/bin/encode_chip_functions.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jsalignon/cactus/HEAD/scripts/create_references/bin/encode_chip_functions.R -------------------------------------------------------------------------------- /scripts/create_references/bin/get_blacklisted_ensembl_file.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jsalignon/cactus/HEAD/scripts/create_references/bin/get_blacklisted_ensembl_file.sh -------------------------------------------------------------------------------- /scripts/create_references/bin/get_fasta_and_gff.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jsalignon/cactus/HEAD/scripts/create_references/bin/get_fasta_and_gff.sh -------------------------------------------------------------------------------- /scripts/create_references/bin/get_linebreak.R: -------------------------------------------------------------------------------- 1 | 2 | get_lb <- function() '\n' 3 | -------------------------------------------------------------------------------- /scripts/create_references/bin/get_tab.R: -------------------------------------------------------------------------------- 1 | 2 | get_tab <- function() '\t' 3 | -------------------------------------------------------------------------------- /scripts/create_references/bin/get_tab.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jsalignon/cactus/HEAD/scripts/create_references/bin/get_tab.sh -------------------------------------------------------------------------------- /scripts/create_references/bin/make_chip_ontology_groups_functions.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jsalignon/cactus/HEAD/scripts/create_references/bin/make_chip_ontology_groups_functions.R -------------------------------------------------------------------------------- /scripts/create_references/bin/make_timestamp.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jsalignon/cactus/HEAD/scripts/create_references/bin/make_timestamp.R -------------------------------------------------------------------------------- /scripts/create_references/conf/containers.config: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jsalignon/cactus/HEAD/scripts/create_references/conf/containers.config -------------------------------------------------------------------------------- /scripts/create_references/conf/reports.config: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jsalignon/cactus/HEAD/scripts/create_references/conf/reports.config -------------------------------------------------------------------------------- /scripts/create_references/create_references.nf: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jsalignon/cactus/HEAD/scripts/create_references/create_references.nf -------------------------------------------------------------------------------- /scripts/create_references/nextflow.config: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jsalignon/cactus/HEAD/scripts/create_references/nextflow.config -------------------------------------------------------------------------------- /scripts/create_test_datasets/bin/0__initialization.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jsalignon/cactus/HEAD/scripts/create_test_datasets/bin/0__initialization.sh -------------------------------------------------------------------------------- /scripts/create_test_datasets/bin/1__get_fastq.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jsalignon/cactus/HEAD/scripts/create_test_datasets/bin/1__get_fastq.sh -------------------------------------------------------------------------------- /scripts/create_test_datasets/bin/2__subsample_reads.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jsalignon/cactus/HEAD/scripts/create_test_datasets/bin/2__subsample_reads.sh -------------------------------------------------------------------------------- /scripts/create_test_datasets/bin/3__make_design_files__fly.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jsalignon/cactus/HEAD/scripts/create_test_datasets/bin/3__make_design_files__fly.sh -------------------------------------------------------------------------------- /scripts/create_test_datasets/bin/3__make_design_files__human.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jsalignon/cactus/HEAD/scripts/create_test_datasets/bin/3__make_design_files__human.sh -------------------------------------------------------------------------------- /scripts/create_test_datasets/bin/3__make_design_files__mouse.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jsalignon/cactus/HEAD/scripts/create_test_datasets/bin/3__make_design_files__mouse.sh -------------------------------------------------------------------------------- /scripts/create_test_datasets/bin/3__make_design_files__worm.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jsalignon/cactus/HEAD/scripts/create_test_datasets/bin/3__make_design_files__worm.sh -------------------------------------------------------------------------------- /scripts/create_test_datasets/bin/create_test_datasets_functions.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jsalignon/cactus/HEAD/scripts/create_test_datasets/bin/create_test_datasets_functions.sh -------------------------------------------------------------------------------- /scripts/create_test_datasets/bin/make_application_note_dirs.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jsalignon/cactus/HEAD/scripts/create_test_datasets/bin/make_application_note_dirs.sh -------------------------------------------------------------------------------- /scripts/create_test_datasets/bin/nextflow.config: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jsalignon/cactus/HEAD/scripts/create_test_datasets/bin/nextflow.config -------------------------------------------------------------------------------- /scripts/create_test_datasets/bin/subsample_reads.nf: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jsalignon/cactus/HEAD/scripts/create_test_datasets/bin/subsample_reads.nf -------------------------------------------------------------------------------- /scripts/create_test_datasets/create_test_datasets.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jsalignon/cactus/HEAD/scripts/create_test_datasets/create_test_datasets.sh -------------------------------------------------------------------------------- /scripts/create_test_datasets/datasets_details.plain: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jsalignon/cactus/HEAD/scripts/create_test_datasets/datasets_details.plain -------------------------------------------------------------------------------- /scripts/create_test_datasets/samples_ids/gsm_accession/gsm_fly.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jsalignon/cactus/HEAD/scripts/create_test_datasets/samples_ids/gsm_accession/gsm_fly.txt -------------------------------------------------------------------------------- /scripts/create_test_datasets/samples_ids/gsm_accession/gsm_human.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jsalignon/cactus/HEAD/scripts/create_test_datasets/samples_ids/gsm_accession/gsm_human.txt -------------------------------------------------------------------------------- /scripts/create_test_datasets/samples_ids/gsm_accession/gsm_mouse.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jsalignon/cactus/HEAD/scripts/create_test_datasets/samples_ids/gsm_accession/gsm_mouse.txt -------------------------------------------------------------------------------- /scripts/create_test_datasets/samples_ids/gsm_accession/gsm_mouse__details.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jsalignon/cactus/HEAD/scripts/create_test_datasets/samples_ids/gsm_accession/gsm_mouse__details.txt -------------------------------------------------------------------------------- /scripts/create_test_datasets/samples_ids/gsm_accession/gsm_test.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jsalignon/cactus/HEAD/scripts/create_test_datasets/samples_ids/gsm_accession/gsm_test.txt -------------------------------------------------------------------------------- /scripts/create_test_datasets/samples_ids/gsm_accession/gsm_worm.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jsalignon/cactus/HEAD/scripts/create_test_datasets/samples_ids/gsm_accession/gsm_worm.txt -------------------------------------------------------------------------------- /scripts/create_test_datasets/samples_ids/gsm_accession/gsm_worm_case_study.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jsalignon/cactus/HEAD/scripts/create_test_datasets/samples_ids/gsm_accession/gsm_worm_case_study.txt -------------------------------------------------------------------------------- /scripts/create_test_datasets/samples_ids/preprocessing/report/genome_and_transcriptome_size.txt: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /scripts/create_test_datasets/samples_ids/srr_accession/srr_fly.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jsalignon/cactus/HEAD/scripts/create_test_datasets/samples_ids/srr_accession/srr_fly.txt -------------------------------------------------------------------------------- /scripts/create_test_datasets/samples_ids/srr_accession/srr_human.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jsalignon/cactus/HEAD/scripts/create_test_datasets/samples_ids/srr_accession/srr_human.txt -------------------------------------------------------------------------------- /scripts/create_test_datasets/samples_ids/srr_accession/srr_mouse.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jsalignon/cactus/HEAD/scripts/create_test_datasets/samples_ids/srr_accession/srr_mouse.txt -------------------------------------------------------------------------------- /scripts/create_test_datasets/samples_ids/srr_accession/srr_test.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jsalignon/cactus/HEAD/scripts/create_test_datasets/samples_ids/srr_accession/srr_test.txt -------------------------------------------------------------------------------- /scripts/create_test_datasets/samples_ids/srr_accession/srr_worm.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jsalignon/cactus/HEAD/scripts/create_test_datasets/samples_ids/srr_accession/srr_worm.txt -------------------------------------------------------------------------------- /scripts/create_test_datasets/samples_ids/srr_accession/srr_worm_case_study.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jsalignon/cactus/HEAD/scripts/create_test_datasets/samples_ids/srr_accession/srr_worm_case_study.txt -------------------------------------------------------------------------------- /scripts/download/download.nf: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jsalignon/cactus/HEAD/scripts/download/download.nf -------------------------------------------------------------------------------- /scripts/download/files.config: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jsalignon/cactus/HEAD/scripts/download/files.config -------------------------------------------------------------------------------- /scripts/download/nextflow.config: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jsalignon/cactus/HEAD/scripts/download/nextflow.config -------------------------------------------------------------------------------- /test_datasets/fly/design/atac_fastq.tsv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jsalignon/cactus/HEAD/test_datasets/fly/design/atac_fastq.tsv -------------------------------------------------------------------------------- /test_datasets/fly/design/comparisons.tsv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jsalignon/cactus/HEAD/test_datasets/fly/design/comparisons.tsv -------------------------------------------------------------------------------- /test_datasets/fly/design/genes_to_remove.tsv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jsalignon/cactus/HEAD/test_datasets/fly/design/genes_to_remove.tsv -------------------------------------------------------------------------------- /test_datasets/fly/design/genes_to_remove_empty.tsv: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /test_datasets/fly/design/groups.tsv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jsalignon/cactus/HEAD/test_datasets/fly/design/groups.tsv -------------------------------------------------------------------------------- /test_datasets/fly/design/mrna_fastq.tsv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jsalignon/cactus/HEAD/test_datasets/fly/design/mrna_fastq.tsv -------------------------------------------------------------------------------- /test_datasets/fly/design/regions_to_remove.tsv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jsalignon/cactus/HEAD/test_datasets/fly/design/regions_to_remove.tsv -------------------------------------------------------------------------------- /test_datasets/fly/parameters/full_test.yml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jsalignon/cactus/HEAD/test_datasets/fly/parameters/full_test.yml -------------------------------------------------------------------------------- /test_datasets/fly/parameters/no_enrich.yml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jsalignon/cactus/HEAD/test_datasets/fly/parameters/no_enrich.yml -------------------------------------------------------------------------------- /test_datasets/fly/parameters/no_enrich__no_gtr.yml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jsalignon/cactus/HEAD/test_datasets/fly/parameters/no_enrich__no_gtr.yml -------------------------------------------------------------------------------- /test_datasets/human/design/atac_fastq.tsv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jsalignon/cactus/HEAD/test_datasets/human/design/atac_fastq.tsv -------------------------------------------------------------------------------- /test_datasets/human/design/comparisons.tsv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jsalignon/cactus/HEAD/test_datasets/human/design/comparisons.tsv -------------------------------------------------------------------------------- /test_datasets/human/design/genes_to_remove.tsv: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /test_datasets/human/design/groups.tsv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jsalignon/cactus/HEAD/test_datasets/human/design/groups.tsv -------------------------------------------------------------------------------- /test_datasets/human/design/mrna_fastq.tsv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jsalignon/cactus/HEAD/test_datasets/human/design/mrna_fastq.tsv -------------------------------------------------------------------------------- /test_datasets/human/design/regions_to_remove.tsv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jsalignon/cactus/HEAD/test_datasets/human/design/regions_to_remove.tsv -------------------------------------------------------------------------------- /test_datasets/human/parameters/full_test.yml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jsalignon/cactus/HEAD/test_datasets/human/parameters/full_test.yml -------------------------------------------------------------------------------- /test_datasets/human/parameters/no_enrich.yml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jsalignon/cactus/HEAD/test_datasets/human/parameters/no_enrich.yml -------------------------------------------------------------------------------- /test_datasets/mouse/design/atac_fastq.tsv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jsalignon/cactus/HEAD/test_datasets/mouse/design/atac_fastq.tsv -------------------------------------------------------------------------------- /test_datasets/mouse/design/comparisons.tsv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jsalignon/cactus/HEAD/test_datasets/mouse/design/comparisons.tsv -------------------------------------------------------------------------------- /test_datasets/mouse/design/genes_to_remove.tsv: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /test_datasets/mouse/design/groups.tsv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jsalignon/cactus/HEAD/test_datasets/mouse/design/groups.tsv -------------------------------------------------------------------------------- /test_datasets/mouse/design/mrna_fastq.tsv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jsalignon/cactus/HEAD/test_datasets/mouse/design/mrna_fastq.tsv -------------------------------------------------------------------------------- /test_datasets/mouse/design/regions_to_remove.tsv: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /test_datasets/mouse/parameters/full_test.yml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jsalignon/cactus/HEAD/test_datasets/mouse/parameters/full_test.yml -------------------------------------------------------------------------------- /test_datasets/mouse/parameters/no_enrich.yml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jsalignon/cactus/HEAD/test_datasets/mouse/parameters/no_enrich.yml -------------------------------------------------------------------------------- /test_datasets/running_the_case_study.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jsalignon/cactus/HEAD/test_datasets/running_the_case_study.sh -------------------------------------------------------------------------------- /test_datasets/running_the_test_datasets.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jsalignon/cactus/HEAD/test_datasets/running_the_test_datasets.sh -------------------------------------------------------------------------------- /test_datasets/worm/design/atac_fastq.tsv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jsalignon/cactus/HEAD/test_datasets/worm/design/atac_fastq.tsv -------------------------------------------------------------------------------- /test_datasets/worm/design/atac_fastq__with_input.tsv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jsalignon/cactus/HEAD/test_datasets/worm/design/atac_fastq__with_input.tsv -------------------------------------------------------------------------------- /test_datasets/worm/design/atac_fastq__without_input.tsv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jsalignon/cactus/HEAD/test_datasets/worm/design/atac_fastq__without_input.tsv -------------------------------------------------------------------------------- /test_datasets/worm/design/comparisons.tsv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jsalignon/cactus/HEAD/test_datasets/worm/design/comparisons.tsv -------------------------------------------------------------------------------- /test_datasets/worm/design/genes_to_remove.tsv: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /test_datasets/worm/design/groups.tsv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jsalignon/cactus/HEAD/test_datasets/worm/design/groups.tsv -------------------------------------------------------------------------------- /test_datasets/worm/design/mrna_fastq.tsv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jsalignon/cactus/HEAD/test_datasets/worm/design/mrna_fastq.tsv -------------------------------------------------------------------------------- /test_datasets/worm/design/regions_to_remove.tsv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jsalignon/cactus/HEAD/test_datasets/worm/design/regions_to_remove.tsv -------------------------------------------------------------------------------- /test_datasets/worm/design/regions_to_remove_empty.tsv: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /test_datasets/worm/parameters/enrich_only_chip.yml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jsalignon/cactus/HEAD/test_datasets/worm/parameters/enrich_only_chip.yml -------------------------------------------------------------------------------- /test_datasets/worm/parameters/enrich_only_genes_self.yml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jsalignon/cactus/HEAD/test_datasets/worm/parameters/enrich_only_genes_self.yml -------------------------------------------------------------------------------- /test_datasets/worm/parameters/enrich_only_genes_self__FDR.yml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jsalignon/cactus/HEAD/test_datasets/worm/parameters/enrich_only_genes_self__FDR.yml -------------------------------------------------------------------------------- /test_datasets/worm/parameters/full_test.yml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jsalignon/cactus/HEAD/test_datasets/worm/parameters/full_test.yml -------------------------------------------------------------------------------- /test_datasets/worm/parameters/no_enrich.yml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jsalignon/cactus/HEAD/test_datasets/worm/parameters/no_enrich.yml -------------------------------------------------------------------------------- /test_datasets/worm/parameters/no_enrich__no_rtr.yml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jsalignon/cactus/HEAD/test_datasets/worm/parameters/no_enrich__no_rtr.yml --------------------------------------------------------------------------------