├── .github └── workflows │ └── publish_site.yml ├── .gitignore ├── LICENSE.md ├── README.md ├── _extensions └── cambiotraining │ ├── courseformat │ ├── _extension.yml │ ├── footer.html │ ├── img │ │ ├── university-of-cambridge-favicon.ico │ │ └── university_crest_reversed.png │ ├── star_levels.lua │ └── theme.scss │ └── fontawesome │ ├── _extension.yml │ ├── assets │ ├── css │ │ ├── all.css │ │ └── latex-fontsize.css │ └── webfonts │ │ ├── fa-brands-400.ttf │ │ ├── fa-brands-400.woff2 │ │ ├── fa-regular-400.ttf │ │ ├── fa-regular-400.woff2 │ │ ├── fa-solid-900.ttf │ │ ├── fa-solid-900.woff2 │ │ ├── fa-v4compatibility.ttf │ │ └── fa-v4compatibility.woff2 │ └── fontawesome.lua ├── _freeze ├── materials │ ├── 02-peak_ranges │ │ ├── execute-results │ │ │ └── html.json │ │ └── figure-html │ │ │ ├── annotation_barplot-1.png │ │ │ ├── ex_answer_h2bub1-1.png │ │ │ ├── ex_answer_h2bub1-2.png │ │ │ ├── h2bub1_exercise_solution-1.png │ │ │ ├── heatmap_exercise_answer-1.png │ │ │ ├── peak_coverage-1.png │ │ │ ├── profile_heatmap-1.png │ │ │ ├── unnamed-chunk-4-1.png │ │ │ ├── unnamed-chunk-6-1.png │ │ │ └── unnamed-chunk-8-1.png │ ├── 03-profile_heatmaps │ │ ├── execute-results │ │ │ └── html.json │ │ └── figure-html │ │ │ ├── enriched_heatmap-1.png │ │ │ ├── ex_answer_heatmap_part2-1.png │ │ │ └── profile_degs-1.png │ └── 04-diffbind │ │ ├── execute-results │ │ └── html.json │ │ └── figure-html │ │ ├── boxplot-1.png │ │ ├── count-1.png │ │ ├── ex_answer_part3-1.png │ │ ├── ex_answer_part3-2.png │ │ ├── ex_answer_part3-3.png │ │ ├── ex_answer_part3-4.png │ │ ├── ex_answer_part3-5.png │ │ ├── heatmap-1.png │ │ ├── plot_ma-1.png │ │ ├── plot_pca-1.png │ │ └── plot_raw-1.png └── site_libs │ └── clipboard │ └── clipboard.min.js ├── _quarto.yml ├── chipseq.Rproj ├── chipseq.code-workspace ├── course_files ├── participants │ ├── data │ │ └── .gitignore │ └── scripts │ │ ├── 01-chipseq_workflow.sh │ │ ├── 02-peak_ranges.R │ │ ├── 03-profile_heatmaps.R │ │ └── 04-diffbind.R └── trainers │ └── README.md ├── index.md ├── materials.md ├── materials ├── 00-template.md ├── 01-peak_calling.md ├── 02-peak_ranges.Rmd ├── 03-profile_heatmaps.Rmd ├── 04-diffbind.Rmd ├── _chapters.yml ├── _sidebar.yml ├── appendix │ └── biomart.Rmd ├── images │ └── igv_screenshot.png └── metro.svg ├── setup.md └── utilities └── prep_data ├── 00-fastqdump.sh ├── 01-download_reference.sh ├── 02-run_chipseq_workflow.sh ├── 03-downsample_fastq.sh ├── 03-sample_bams.sh ├── 04-homer_motifs.sh ├── 05-diffbind.sh ├── 06-prepare_participant_files.sh ├── chip_environment.yml ├── diffbind_samplesheet.csv ├── nagarajan2014_sra_accessions.csv └── samplesheet.csv /.github/workflows/publish_site.yml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cambiotraining/chipseq/HEAD/.github/workflows/publish_site.yml -------------------------------------------------------------------------------- /.gitignore: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cambiotraining/chipseq/HEAD/.gitignore -------------------------------------------------------------------------------- /LICENSE.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cambiotraining/chipseq/HEAD/LICENSE.md -------------------------------------------------------------------------------- /README.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cambiotraining/chipseq/HEAD/README.md -------------------------------------------------------------------------------- /_extensions/cambiotraining/courseformat/_extension.yml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cambiotraining/chipseq/HEAD/_extensions/cambiotraining/courseformat/_extension.yml -------------------------------------------------------------------------------- /_extensions/cambiotraining/courseformat/footer.html: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cambiotraining/chipseq/HEAD/_extensions/cambiotraining/courseformat/footer.html -------------------------------------------------------------------------------- /_extensions/cambiotraining/courseformat/img/university-of-cambridge-favicon.ico: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cambiotraining/chipseq/HEAD/_extensions/cambiotraining/courseformat/img/university-of-cambridge-favicon.ico -------------------------------------------------------------------------------- /_extensions/cambiotraining/courseformat/img/university_crest_reversed.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cambiotraining/chipseq/HEAD/_extensions/cambiotraining/courseformat/img/university_crest_reversed.png -------------------------------------------------------------------------------- /_extensions/cambiotraining/courseformat/star_levels.lua: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cambiotraining/chipseq/HEAD/_extensions/cambiotraining/courseformat/star_levels.lua -------------------------------------------------------------------------------- /_extensions/cambiotraining/courseformat/theme.scss: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cambiotraining/chipseq/HEAD/_extensions/cambiotraining/courseformat/theme.scss -------------------------------------------------------------------------------- /_extensions/cambiotraining/fontawesome/_extension.yml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cambiotraining/chipseq/HEAD/_extensions/cambiotraining/fontawesome/_extension.yml -------------------------------------------------------------------------------- /_extensions/cambiotraining/fontawesome/assets/css/all.css: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cambiotraining/chipseq/HEAD/_extensions/cambiotraining/fontawesome/assets/css/all.css -------------------------------------------------------------------------------- /_extensions/cambiotraining/fontawesome/assets/css/latex-fontsize.css: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cambiotraining/chipseq/HEAD/_extensions/cambiotraining/fontawesome/assets/css/latex-fontsize.css -------------------------------------------------------------------------------- /_extensions/cambiotraining/fontawesome/assets/webfonts/fa-brands-400.ttf: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cambiotraining/chipseq/HEAD/_extensions/cambiotraining/fontawesome/assets/webfonts/fa-brands-400.ttf -------------------------------------------------------------------------------- /_extensions/cambiotraining/fontawesome/assets/webfonts/fa-brands-400.woff2: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cambiotraining/chipseq/HEAD/_extensions/cambiotraining/fontawesome/assets/webfonts/fa-brands-400.woff2 -------------------------------------------------------------------------------- /_extensions/cambiotraining/fontawesome/assets/webfonts/fa-regular-400.ttf: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cambiotraining/chipseq/HEAD/_extensions/cambiotraining/fontawesome/assets/webfonts/fa-regular-400.ttf -------------------------------------------------------------------------------- /_extensions/cambiotraining/fontawesome/assets/webfonts/fa-regular-400.woff2: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cambiotraining/chipseq/HEAD/_extensions/cambiotraining/fontawesome/assets/webfonts/fa-regular-400.woff2 -------------------------------------------------------------------------------- /_extensions/cambiotraining/fontawesome/assets/webfonts/fa-solid-900.ttf: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cambiotraining/chipseq/HEAD/_extensions/cambiotraining/fontawesome/assets/webfonts/fa-solid-900.ttf -------------------------------------------------------------------------------- /_extensions/cambiotraining/fontawesome/assets/webfonts/fa-solid-900.woff2: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cambiotraining/chipseq/HEAD/_extensions/cambiotraining/fontawesome/assets/webfonts/fa-solid-900.woff2 -------------------------------------------------------------------------------- /_extensions/cambiotraining/fontawesome/assets/webfonts/fa-v4compatibility.ttf: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cambiotraining/chipseq/HEAD/_extensions/cambiotraining/fontawesome/assets/webfonts/fa-v4compatibility.ttf -------------------------------------------------------------------------------- /_extensions/cambiotraining/fontawesome/assets/webfonts/fa-v4compatibility.woff2: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cambiotraining/chipseq/HEAD/_extensions/cambiotraining/fontawesome/assets/webfonts/fa-v4compatibility.woff2 -------------------------------------------------------------------------------- /_extensions/cambiotraining/fontawesome/fontawesome.lua: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cambiotraining/chipseq/HEAD/_extensions/cambiotraining/fontawesome/fontawesome.lua -------------------------------------------------------------------------------- /_freeze/materials/02-peak_ranges/execute-results/html.json: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cambiotraining/chipseq/HEAD/_freeze/materials/02-peak_ranges/execute-results/html.json -------------------------------------------------------------------------------- /_freeze/materials/02-peak_ranges/figure-html/annotation_barplot-1.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cambiotraining/chipseq/HEAD/_freeze/materials/02-peak_ranges/figure-html/annotation_barplot-1.png -------------------------------------------------------------------------------- /_freeze/materials/02-peak_ranges/figure-html/ex_answer_h2bub1-1.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cambiotraining/chipseq/HEAD/_freeze/materials/02-peak_ranges/figure-html/ex_answer_h2bub1-1.png -------------------------------------------------------------------------------- /_freeze/materials/02-peak_ranges/figure-html/ex_answer_h2bub1-2.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cambiotraining/chipseq/HEAD/_freeze/materials/02-peak_ranges/figure-html/ex_answer_h2bub1-2.png -------------------------------------------------------------------------------- /_freeze/materials/02-peak_ranges/figure-html/h2bub1_exercise_solution-1.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cambiotraining/chipseq/HEAD/_freeze/materials/02-peak_ranges/figure-html/h2bub1_exercise_solution-1.png -------------------------------------------------------------------------------- /_freeze/materials/02-peak_ranges/figure-html/heatmap_exercise_answer-1.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cambiotraining/chipseq/HEAD/_freeze/materials/02-peak_ranges/figure-html/heatmap_exercise_answer-1.png -------------------------------------------------------------------------------- /_freeze/materials/02-peak_ranges/figure-html/peak_coverage-1.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cambiotraining/chipseq/HEAD/_freeze/materials/02-peak_ranges/figure-html/peak_coverage-1.png -------------------------------------------------------------------------------- /_freeze/materials/02-peak_ranges/figure-html/profile_heatmap-1.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cambiotraining/chipseq/HEAD/_freeze/materials/02-peak_ranges/figure-html/profile_heatmap-1.png -------------------------------------------------------------------------------- /_freeze/materials/02-peak_ranges/figure-html/unnamed-chunk-4-1.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cambiotraining/chipseq/HEAD/_freeze/materials/02-peak_ranges/figure-html/unnamed-chunk-4-1.png -------------------------------------------------------------------------------- /_freeze/materials/02-peak_ranges/figure-html/unnamed-chunk-6-1.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cambiotraining/chipseq/HEAD/_freeze/materials/02-peak_ranges/figure-html/unnamed-chunk-6-1.png -------------------------------------------------------------------------------- /_freeze/materials/02-peak_ranges/figure-html/unnamed-chunk-8-1.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cambiotraining/chipseq/HEAD/_freeze/materials/02-peak_ranges/figure-html/unnamed-chunk-8-1.png -------------------------------------------------------------------------------- /_freeze/materials/03-profile_heatmaps/execute-results/html.json: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cambiotraining/chipseq/HEAD/_freeze/materials/03-profile_heatmaps/execute-results/html.json -------------------------------------------------------------------------------- /_freeze/materials/03-profile_heatmaps/figure-html/enriched_heatmap-1.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cambiotraining/chipseq/HEAD/_freeze/materials/03-profile_heatmaps/figure-html/enriched_heatmap-1.png -------------------------------------------------------------------------------- /_freeze/materials/03-profile_heatmaps/figure-html/ex_answer_heatmap_part2-1.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cambiotraining/chipseq/HEAD/_freeze/materials/03-profile_heatmaps/figure-html/ex_answer_heatmap_part2-1.png -------------------------------------------------------------------------------- /_freeze/materials/03-profile_heatmaps/figure-html/profile_degs-1.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cambiotraining/chipseq/HEAD/_freeze/materials/03-profile_heatmaps/figure-html/profile_degs-1.png -------------------------------------------------------------------------------- /_freeze/materials/04-diffbind/execute-results/html.json: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cambiotraining/chipseq/HEAD/_freeze/materials/04-diffbind/execute-results/html.json -------------------------------------------------------------------------------- /_freeze/materials/04-diffbind/figure-html/boxplot-1.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cambiotraining/chipseq/HEAD/_freeze/materials/04-diffbind/figure-html/boxplot-1.png -------------------------------------------------------------------------------- /_freeze/materials/04-diffbind/figure-html/count-1.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cambiotraining/chipseq/HEAD/_freeze/materials/04-diffbind/figure-html/count-1.png -------------------------------------------------------------------------------- /_freeze/materials/04-diffbind/figure-html/ex_answer_part3-1.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cambiotraining/chipseq/HEAD/_freeze/materials/04-diffbind/figure-html/ex_answer_part3-1.png -------------------------------------------------------------------------------- /_freeze/materials/04-diffbind/figure-html/ex_answer_part3-2.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cambiotraining/chipseq/HEAD/_freeze/materials/04-diffbind/figure-html/ex_answer_part3-2.png -------------------------------------------------------------------------------- /_freeze/materials/04-diffbind/figure-html/ex_answer_part3-3.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cambiotraining/chipseq/HEAD/_freeze/materials/04-diffbind/figure-html/ex_answer_part3-3.png -------------------------------------------------------------------------------- /_freeze/materials/04-diffbind/figure-html/ex_answer_part3-4.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cambiotraining/chipseq/HEAD/_freeze/materials/04-diffbind/figure-html/ex_answer_part3-4.png -------------------------------------------------------------------------------- /_freeze/materials/04-diffbind/figure-html/ex_answer_part3-5.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cambiotraining/chipseq/HEAD/_freeze/materials/04-diffbind/figure-html/ex_answer_part3-5.png -------------------------------------------------------------------------------- /_freeze/materials/04-diffbind/figure-html/heatmap-1.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cambiotraining/chipseq/HEAD/_freeze/materials/04-diffbind/figure-html/heatmap-1.png -------------------------------------------------------------------------------- /_freeze/materials/04-diffbind/figure-html/plot_ma-1.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cambiotraining/chipseq/HEAD/_freeze/materials/04-diffbind/figure-html/plot_ma-1.png -------------------------------------------------------------------------------- /_freeze/materials/04-diffbind/figure-html/plot_pca-1.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cambiotraining/chipseq/HEAD/_freeze/materials/04-diffbind/figure-html/plot_pca-1.png -------------------------------------------------------------------------------- /_freeze/materials/04-diffbind/figure-html/plot_raw-1.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cambiotraining/chipseq/HEAD/_freeze/materials/04-diffbind/figure-html/plot_raw-1.png -------------------------------------------------------------------------------- /_freeze/site_libs/clipboard/clipboard.min.js: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cambiotraining/chipseq/HEAD/_freeze/site_libs/clipboard/clipboard.min.js -------------------------------------------------------------------------------- /_quarto.yml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cambiotraining/chipseq/HEAD/_quarto.yml -------------------------------------------------------------------------------- /chipseq.Rproj: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cambiotraining/chipseq/HEAD/chipseq.Rproj -------------------------------------------------------------------------------- /chipseq.code-workspace: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cambiotraining/chipseq/HEAD/chipseq.code-workspace -------------------------------------------------------------------------------- /course_files/participants/data/.gitignore: -------------------------------------------------------------------------------- 1 | * 2 | */ 3 | !README* 4 | !.gitignore 5 | -------------------------------------------------------------------------------- /course_files/participants/scripts/01-chipseq_workflow.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cambiotraining/chipseq/HEAD/course_files/participants/scripts/01-chipseq_workflow.sh -------------------------------------------------------------------------------- /course_files/participants/scripts/02-peak_ranges.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cambiotraining/chipseq/HEAD/course_files/participants/scripts/02-peak_ranges.R -------------------------------------------------------------------------------- /course_files/participants/scripts/03-profile_heatmaps.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cambiotraining/chipseq/HEAD/course_files/participants/scripts/03-profile_heatmaps.R -------------------------------------------------------------------------------- /course_files/participants/scripts/04-diffbind.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cambiotraining/chipseq/HEAD/course_files/participants/scripts/04-diffbind.R -------------------------------------------------------------------------------- /course_files/trainers/README.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cambiotraining/chipseq/HEAD/course_files/trainers/README.md -------------------------------------------------------------------------------- /index.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cambiotraining/chipseq/HEAD/index.md -------------------------------------------------------------------------------- /materials.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cambiotraining/chipseq/HEAD/materials.md -------------------------------------------------------------------------------- /materials/00-template.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cambiotraining/chipseq/HEAD/materials/00-template.md -------------------------------------------------------------------------------- /materials/01-peak_calling.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cambiotraining/chipseq/HEAD/materials/01-peak_calling.md -------------------------------------------------------------------------------- /materials/02-peak_ranges.Rmd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cambiotraining/chipseq/HEAD/materials/02-peak_ranges.Rmd -------------------------------------------------------------------------------- /materials/03-profile_heatmaps.Rmd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cambiotraining/chipseq/HEAD/materials/03-profile_heatmaps.Rmd -------------------------------------------------------------------------------- /materials/04-diffbind.Rmd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cambiotraining/chipseq/HEAD/materials/04-diffbind.Rmd -------------------------------------------------------------------------------- /materials/_chapters.yml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cambiotraining/chipseq/HEAD/materials/_chapters.yml -------------------------------------------------------------------------------- /materials/_sidebar.yml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cambiotraining/chipseq/HEAD/materials/_sidebar.yml -------------------------------------------------------------------------------- /materials/appendix/biomart.Rmd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cambiotraining/chipseq/HEAD/materials/appendix/biomart.Rmd -------------------------------------------------------------------------------- /materials/images/igv_screenshot.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cambiotraining/chipseq/HEAD/materials/images/igv_screenshot.png -------------------------------------------------------------------------------- /materials/metro.svg: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cambiotraining/chipseq/HEAD/materials/metro.svg -------------------------------------------------------------------------------- /setup.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cambiotraining/chipseq/HEAD/setup.md -------------------------------------------------------------------------------- /utilities/prep_data/00-fastqdump.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cambiotraining/chipseq/HEAD/utilities/prep_data/00-fastqdump.sh -------------------------------------------------------------------------------- /utilities/prep_data/01-download_reference.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cambiotraining/chipseq/HEAD/utilities/prep_data/01-download_reference.sh -------------------------------------------------------------------------------- /utilities/prep_data/02-run_chipseq_workflow.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cambiotraining/chipseq/HEAD/utilities/prep_data/02-run_chipseq_workflow.sh -------------------------------------------------------------------------------- /utilities/prep_data/03-downsample_fastq.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cambiotraining/chipseq/HEAD/utilities/prep_data/03-downsample_fastq.sh -------------------------------------------------------------------------------- /utilities/prep_data/03-sample_bams.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cambiotraining/chipseq/HEAD/utilities/prep_data/03-sample_bams.sh -------------------------------------------------------------------------------- /utilities/prep_data/04-homer_motifs.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cambiotraining/chipseq/HEAD/utilities/prep_data/04-homer_motifs.sh -------------------------------------------------------------------------------- /utilities/prep_data/05-diffbind.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cambiotraining/chipseq/HEAD/utilities/prep_data/05-diffbind.sh -------------------------------------------------------------------------------- /utilities/prep_data/06-prepare_participant_files.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cambiotraining/chipseq/HEAD/utilities/prep_data/06-prepare_participant_files.sh -------------------------------------------------------------------------------- /utilities/prep_data/chip_environment.yml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cambiotraining/chipseq/HEAD/utilities/prep_data/chip_environment.yml -------------------------------------------------------------------------------- /utilities/prep_data/diffbind_samplesheet.csv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cambiotraining/chipseq/HEAD/utilities/prep_data/diffbind_samplesheet.csv -------------------------------------------------------------------------------- /utilities/prep_data/nagarajan2014_sra_accessions.csv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cambiotraining/chipseq/HEAD/utilities/prep_data/nagarajan2014_sra_accessions.csv -------------------------------------------------------------------------------- /utilities/prep_data/samplesheet.csv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cambiotraining/chipseq/HEAD/utilities/prep_data/samplesheet.csv --------------------------------------------------------------------------------