├── .bundle └── config ├── .gitignore ├── .ruby-version ├── CITATION.cff ├── Dockerfile ├── GENE_COUNT_TABLE_IMPLEMENTATION.md ├── Gemfile ├── Gemfile.lock ├── LAYOUT_REFACTORING.md ├── LICENSE.txt ├── README.md ├── Rakefile ├── app.rb ├── config.ru ├── config └── database.yml ├── db ├── migrate │ ├── 20150415101305_create_experiments.rb │ ├── 20150415101316_create_bedfiles.rb │ ├── 20150623061634_update_experiments.rb │ ├── 20151127141027_create_analysis.rb │ ├── 20151127142537_create_bedsizes.rb │ └── 20151128015049_create_runs.rb └── schema.rb ├── docker-compose.dev.yml ├── docker-compose.yml ├── docs └── setup.md ├── lib ├── pj.rb ├── pj │ ├── analysis.rb │ ├── bedfile.rb │ ├── bedsize.rb │ ├── experiment.rb │ ├── fastqc.rb │ ├── location.rb │ ├── metadata.rb │ ├── run.rb │ └── sra.rb └── tasks │ └── metadata.rake ├── public ├── analysisList.tab ├── css │ ├── all.css │ ├── all.min.css │ ├── bootstrap.min.css │ ├── brands.css │ ├── brands.min.css │ ├── flexselect.css │ ├── fontawesome.css │ ├── fontawesome.min.css │ ├── regular.css │ ├── regular.min.css │ ├── solid.css │ ├── solid.min.css │ ├── svg-with-js.css │ ├── svg-with-js.min.css │ ├── typeaheadjs.css │ ├── v4-font-face.css │ ├── v4-font-face.min.css │ ├── v4-shims.css │ ├── v4-shims.min.css │ ├── v5-font-face.css │ └── v5-font-face.min.css ├── diff-analysis.examples.json ├── examples │ ├── ce10 │ │ ├── bedA.txt │ │ ├── bedB.txt │ │ ├── countA.txt │ │ ├── geneA.txt │ │ ├── geneB.txt │ │ ├── motifA.txt │ │ └── motifB.txt │ ├── ce11 │ │ ├── bedA.txt │ │ ├── bedB.txt │ │ ├── countA.txt │ │ ├── geneA.txt │ │ ├── geneB.txt │ │ ├── motifA.txt │ │ └── motifB.txt │ ├── dm3 │ │ ├── bedA.txt │ │ ├── bedB.txt │ │ ├── countA.txt │ │ ├── geneA.txt │ │ ├── geneB.txt │ │ ├── motifA.txt │ │ └── motifB.txt │ ├── dm6 │ │ ├── bedA.txt │ │ ├── bedB.txt │ │ ├── countA.txt │ │ ├── geneA.txt │ │ ├── geneB.txt │ │ ├── motifA.txt │ │ └── motifB.txt │ ├── hg19 │ │ ├── bedA.txt │ │ ├── bedB.txt │ │ ├── countA.txt │ │ ├── geneA.txt │ │ ├── geneB.txt │ │ ├── motifA.txt │ │ └── motifB.txt │ ├── hg38 │ │ ├── bedA.txt │ │ ├── bedB.txt │ │ ├── countA.txt │ │ ├── geneA.txt │ │ ├── geneB.txt │ │ ├── motifA.txt │ │ └── motifB.txt │ ├── mm10 │ │ ├── bedA.txt │ │ ├── bedB.txt │ │ ├── countA.txt │ │ ├── geneA.txt │ │ ├── geneB.txt │ │ ├── motifA.txt │ │ └── motifB.txt │ ├── mm9 │ │ ├── bedA.txt │ │ ├── bedB.txt │ │ ├── countA.txt │ │ ├── geneA.txt │ │ ├── geneB.txt │ │ ├── motifA.txt │ │ └── motifB.txt │ ├── rn6 │ │ ├── bedA.txt │ │ ├── bedB.txt │ │ ├── countA.txt │ │ ├── geneA.txt │ │ ├── geneB.txt │ │ ├── motifA.txt │ │ └── motifB.txt │ └── sacCer3 │ │ ├── bedA.txt │ │ ├── bedB.txt │ │ ├── countA.txt │ │ ├── geneA.txt │ │ ├── geneB.txt │ │ ├── motifA.txt │ │ └── motifB.txt ├── images │ └── logo │ │ ├── chiba_uni_logo.png │ │ ├── dbcls_logo.png │ │ ├── ddbj_logo.png │ │ ├── jst_logo.png │ │ ├── ku_logo.jpg │ │ ├── kumamoto_uni_logo.jpg │ │ ├── kyoto_uni_logo.png │ │ └── nbdc_logo.png ├── js │ ├── bootstrap.min.js │ ├── ie10-viewport-bug-workaround.js │ ├── jquery.flexselect.js │ ├── jquery.min.js │ ├── liquidmetal.js │ ├── pj │ │ ├── colo.js │ │ ├── diff_analysis.js │ │ ├── diff_analysis_result.js │ │ ├── enrichment_analysis.js │ │ ├── enrichment_analysis_result.js │ │ ├── experiment.js │ │ ├── peak_browser.js │ │ ├── pj.js │ │ ├── search.js │ │ └── target_genes.js │ └── typeahead.bundle.js ├── robots.txt ├── tables │ ├── exp2run.json │ └── lineNum.tsv └── 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 ├── rdf ├── README.md ├── bin │ ├── bed2ttl │ ├── chr2genbank │ ├── rdfize_colo.awk │ └── rdfize_target_genes.awk ├── generate-rdf ├── images │ ├── chipatlas_analysis_rdf.png │ └── chipatlas_bindingsites_rdf.png ├── ontology │ └── cao.ttl └── reference │ ├── GCF_000001215.2_Release_5_assembly_report.txt │ ├── GCF_000001635.18_MGSCv37_assembly_report.txt │ ├── GCF_000001895.5_Rnor_6.0_assembly_report.txt │ ├── GCF_000002985.5_WBcel215_assembly_report.txt │ └── GCF_000146045.2_R64_assembly_report.txt ├── script ├── diff-analysis │ └── diff_analysis_for_ChIP_ATAC_DNase.sh ├── enrichment-analysis │ ├── Dockerfile │ ├── bedToBoundProteins.sh │ ├── btbpToHtml.txt │ ├── docker-compose.yml │ ├── enrichment-analysis.cwl │ ├── enrichment-analysis.sh │ ├── geneList_A.txt │ ├── geneList_B.txt │ ├── job.params.json │ ├── job.reference.json │ ├── job.yml │ └── test.sh ├── launch-instance │ ├── README.md │ ├── launch-chip-atlas.conf.example │ └── launch-chip-atlas.sh ├── sapporo-enrichment-analysis │ ├── docker-compose.yml │ ├── download-references.sh │ └── sapporo_config │ │ ├── run.sh │ │ └── service-info.json ├── systemctl │ ├── README.md │ └── chip-atlas └── update_2025 │ ├── DA │ ├── DA │ ├── README.md │ ├── edgeR.r │ ├── help.txt │ └── make_igv_session.awk │ ├── EA │ ├── EA │ ├── btbpToHtml.txt │ ├── help.txt │ └── tsv_to_html.awk │ └── PAGE │ ├── GRNcreator │ ├── PAGE │ ├── btbpToHtml.txt │ ├── help.txt │ ├── page.R │ └── tsv_to_html.awk ├── test ├── count_functionality_test.js ├── dmr │ ├── dataA.srx │ ├── dataB.srx │ └── dmr.sh └── enrichment_test.html ├── unicorn.rb └── views ├── _navigation.haml ├── about.haml ├── colo.haml ├── diff_analysis.haml ├── diff_analysis_result.haml ├── enrichment_analysis.haml ├── enrichment_analysis_result.haml ├── experiment.haml ├── footer.haml ├── not_found.haml ├── peak_browser.haml ├── publications.haml ├── publications.markdown ├── search.haml ├── style.sass ├── target_genes.haml └── updates.markdown /.bundle/config: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/inutano/chip-atlas/HEAD/.bundle/config -------------------------------------------------------------------------------- /.gitignore: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/inutano/chip-atlas/HEAD/.gitignore -------------------------------------------------------------------------------- /.ruby-version: -------------------------------------------------------------------------------- 1 | 3.2.2 2 | -------------------------------------------------------------------------------- /CITATION.cff: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/inutano/chip-atlas/HEAD/CITATION.cff -------------------------------------------------------------------------------- /Dockerfile: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/inutano/chip-atlas/HEAD/Dockerfile -------------------------------------------------------------------------------- /GENE_COUNT_TABLE_IMPLEMENTATION.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/inutano/chip-atlas/HEAD/GENE_COUNT_TABLE_IMPLEMENTATION.md -------------------------------------------------------------------------------- /Gemfile: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/inutano/chip-atlas/HEAD/Gemfile -------------------------------------------------------------------------------- /Gemfile.lock: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/inutano/chip-atlas/HEAD/Gemfile.lock -------------------------------------------------------------------------------- /LAYOUT_REFACTORING.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/inutano/chip-atlas/HEAD/LAYOUT_REFACTORING.md -------------------------------------------------------------------------------- /LICENSE.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/inutano/chip-atlas/HEAD/LICENSE.txt -------------------------------------------------------------------------------- /README.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/inutano/chip-atlas/HEAD/README.md -------------------------------------------------------------------------------- /Rakefile: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/inutano/chip-atlas/HEAD/Rakefile -------------------------------------------------------------------------------- /app.rb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/inutano/chip-atlas/HEAD/app.rb -------------------------------------------------------------------------------- /config.ru: -------------------------------------------------------------------------------- 1 | require File.dirname(__FILE__) + "/app" 2 | use Rack::RewindableInput::Middleware 3 | run PeakJohn 4 | -------------------------------------------------------------------------------- /config/database.yml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/inutano/chip-atlas/HEAD/config/database.yml -------------------------------------------------------------------------------- /db/migrate/20150415101305_create_experiments.rb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/inutano/chip-atlas/HEAD/db/migrate/20150415101305_create_experiments.rb -------------------------------------------------------------------------------- /db/migrate/20150415101316_create_bedfiles.rb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/inutano/chip-atlas/HEAD/db/migrate/20150415101316_create_bedfiles.rb -------------------------------------------------------------------------------- /db/migrate/20150623061634_update_experiments.rb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/inutano/chip-atlas/HEAD/db/migrate/20150623061634_update_experiments.rb -------------------------------------------------------------------------------- /db/migrate/20151127141027_create_analysis.rb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/inutano/chip-atlas/HEAD/db/migrate/20151127141027_create_analysis.rb -------------------------------------------------------------------------------- /db/migrate/20151127142537_create_bedsizes.rb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/inutano/chip-atlas/HEAD/db/migrate/20151127142537_create_bedsizes.rb -------------------------------------------------------------------------------- /db/migrate/20151128015049_create_runs.rb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/inutano/chip-atlas/HEAD/db/migrate/20151128015049_create_runs.rb -------------------------------------------------------------------------------- /db/schema.rb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/inutano/chip-atlas/HEAD/db/schema.rb -------------------------------------------------------------------------------- /docker-compose.dev.yml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/inutano/chip-atlas/HEAD/docker-compose.dev.yml -------------------------------------------------------------------------------- /docker-compose.yml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/inutano/chip-atlas/HEAD/docker-compose.yml -------------------------------------------------------------------------------- /docs/setup.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/inutano/chip-atlas/HEAD/docs/setup.md -------------------------------------------------------------------------------- /lib/pj.rb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/inutano/chip-atlas/HEAD/lib/pj.rb -------------------------------------------------------------------------------- /lib/pj/analysis.rb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/inutano/chip-atlas/HEAD/lib/pj/analysis.rb -------------------------------------------------------------------------------- /lib/pj/bedfile.rb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/inutano/chip-atlas/HEAD/lib/pj/bedfile.rb -------------------------------------------------------------------------------- /lib/pj/bedsize.rb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/inutano/chip-atlas/HEAD/lib/pj/bedsize.rb -------------------------------------------------------------------------------- /lib/pj/experiment.rb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/inutano/chip-atlas/HEAD/lib/pj/experiment.rb -------------------------------------------------------------------------------- /lib/pj/fastqc.rb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/inutano/chip-atlas/HEAD/lib/pj/fastqc.rb -------------------------------------------------------------------------------- /lib/pj/location.rb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/inutano/chip-atlas/HEAD/lib/pj/location.rb -------------------------------------------------------------------------------- /lib/pj/metadata.rb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/inutano/chip-atlas/HEAD/lib/pj/metadata.rb -------------------------------------------------------------------------------- /lib/pj/run.rb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/inutano/chip-atlas/HEAD/lib/pj/run.rb -------------------------------------------------------------------------------- /lib/pj/sra.rb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/inutano/chip-atlas/HEAD/lib/pj/sra.rb -------------------------------------------------------------------------------- /lib/tasks/metadata.rake: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/inutano/chip-atlas/HEAD/lib/tasks/metadata.rake -------------------------------------------------------------------------------- /public/analysisList.tab: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/inutano/chip-atlas/HEAD/public/analysisList.tab -------------------------------------------------------------------------------- /public/css/all.css: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/inutano/chip-atlas/HEAD/public/css/all.css -------------------------------------------------------------------------------- /public/css/all.min.css: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/inutano/chip-atlas/HEAD/public/css/all.min.css -------------------------------------------------------------------------------- /public/css/bootstrap.min.css: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/inutano/chip-atlas/HEAD/public/css/bootstrap.min.css -------------------------------------------------------------------------------- /public/css/brands.css: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/inutano/chip-atlas/HEAD/public/css/brands.css -------------------------------------------------------------------------------- /public/css/brands.min.css: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/inutano/chip-atlas/HEAD/public/css/brands.min.css -------------------------------------------------------------------------------- /public/css/flexselect.css: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/inutano/chip-atlas/HEAD/public/css/flexselect.css -------------------------------------------------------------------------------- /public/css/fontawesome.css: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/inutano/chip-atlas/HEAD/public/css/fontawesome.css -------------------------------------------------------------------------------- /public/css/fontawesome.min.css: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/inutano/chip-atlas/HEAD/public/css/fontawesome.min.css -------------------------------------------------------------------------------- /public/css/regular.css: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/inutano/chip-atlas/HEAD/public/css/regular.css -------------------------------------------------------------------------------- /public/css/regular.min.css: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/inutano/chip-atlas/HEAD/public/css/regular.min.css -------------------------------------------------------------------------------- /public/css/solid.css: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/inutano/chip-atlas/HEAD/public/css/solid.css -------------------------------------------------------------------------------- /public/css/solid.min.css: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/inutano/chip-atlas/HEAD/public/css/solid.min.css -------------------------------------------------------------------------------- /public/css/svg-with-js.css: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/inutano/chip-atlas/HEAD/public/css/svg-with-js.css -------------------------------------------------------------------------------- /public/css/svg-with-js.min.css: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/inutano/chip-atlas/HEAD/public/css/svg-with-js.min.css -------------------------------------------------------------------------------- /public/css/typeaheadjs.css: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/inutano/chip-atlas/HEAD/public/css/typeaheadjs.css -------------------------------------------------------------------------------- /public/css/v4-font-face.css: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/inutano/chip-atlas/HEAD/public/css/v4-font-face.css -------------------------------------------------------------------------------- /public/css/v4-font-face.min.css: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/inutano/chip-atlas/HEAD/public/css/v4-font-face.min.css -------------------------------------------------------------------------------- /public/css/v4-shims.css: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/inutano/chip-atlas/HEAD/public/css/v4-shims.css -------------------------------------------------------------------------------- /public/css/v4-shims.min.css: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/inutano/chip-atlas/HEAD/public/css/v4-shims.min.css -------------------------------------------------------------------------------- /public/css/v5-font-face.css: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/inutano/chip-atlas/HEAD/public/css/v5-font-face.css -------------------------------------------------------------------------------- /public/css/v5-font-face.min.css: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/inutano/chip-atlas/HEAD/public/css/v5-font-face.min.css -------------------------------------------------------------------------------- /public/diff-analysis.examples.json: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/inutano/chip-atlas/HEAD/public/diff-analysis.examples.json -------------------------------------------------------------------------------- /public/examples/ce10/bedA.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/inutano/chip-atlas/HEAD/public/examples/ce10/bedA.txt -------------------------------------------------------------------------------- /public/examples/ce10/bedB.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/inutano/chip-atlas/HEAD/public/examples/ce10/bedB.txt -------------------------------------------------------------------------------- /public/examples/ce10/countA.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/inutano/chip-atlas/HEAD/public/examples/ce10/countA.txt -------------------------------------------------------------------------------- /public/examples/ce10/geneA.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/inutano/chip-atlas/HEAD/public/examples/ce10/geneA.txt -------------------------------------------------------------------------------- /public/examples/ce10/geneB.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/inutano/chip-atlas/HEAD/public/examples/ce10/geneB.txt -------------------------------------------------------------------------------- /public/examples/ce10/motifA.txt: -------------------------------------------------------------------------------- 1 | TRTTTACTTW 2 | -------------------------------------------------------------------------------- /public/examples/ce10/motifB.txt: -------------------------------------------------------------------------------- 1 | TRTTTGCTGA 2 | -------------------------------------------------------------------------------- /public/examples/ce11/bedA.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/inutano/chip-atlas/HEAD/public/examples/ce11/bedA.txt -------------------------------------------------------------------------------- /public/examples/ce11/bedB.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/inutano/chip-atlas/HEAD/public/examples/ce11/bedB.txt -------------------------------------------------------------------------------- /public/examples/ce11/countA.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/inutano/chip-atlas/HEAD/public/examples/ce11/countA.txt -------------------------------------------------------------------------------- /public/examples/ce11/geneA.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/inutano/chip-atlas/HEAD/public/examples/ce11/geneA.txt -------------------------------------------------------------------------------- /public/examples/ce11/geneB.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/inutano/chip-atlas/HEAD/public/examples/ce11/geneB.txt -------------------------------------------------------------------------------- /public/examples/ce11/motifA.txt: -------------------------------------------------------------------------------- 1 | TRTTTACTTW 2 | -------------------------------------------------------------------------------- /public/examples/ce11/motifB.txt: -------------------------------------------------------------------------------- 1 | TRTTTGCTGA 2 | -------------------------------------------------------------------------------- /public/examples/dm3/bedA.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/inutano/chip-atlas/HEAD/public/examples/dm3/bedA.txt -------------------------------------------------------------------------------- /public/examples/dm3/bedB.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/inutano/chip-atlas/HEAD/public/examples/dm3/bedB.txt -------------------------------------------------------------------------------- /public/examples/dm3/countA.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/inutano/chip-atlas/HEAD/public/examples/dm3/countA.txt -------------------------------------------------------------------------------- /public/examples/dm3/geneA.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/inutano/chip-atlas/HEAD/public/examples/dm3/geneA.txt -------------------------------------------------------------------------------- /public/examples/dm3/geneB.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/inutano/chip-atlas/HEAD/public/examples/dm3/geneB.txt -------------------------------------------------------------------------------- /public/examples/dm3/motifA.txt: -------------------------------------------------------------------------------- 1 | TRTTTACTTW 2 | -------------------------------------------------------------------------------- /public/examples/dm3/motifB.txt: -------------------------------------------------------------------------------- 1 | TRTTTGCTGA 2 | -------------------------------------------------------------------------------- /public/examples/dm6/bedA.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/inutano/chip-atlas/HEAD/public/examples/dm6/bedA.txt -------------------------------------------------------------------------------- /public/examples/dm6/bedB.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/inutano/chip-atlas/HEAD/public/examples/dm6/bedB.txt -------------------------------------------------------------------------------- /public/examples/dm6/countA.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/inutano/chip-atlas/HEAD/public/examples/dm6/countA.txt -------------------------------------------------------------------------------- /public/examples/dm6/geneA.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/inutano/chip-atlas/HEAD/public/examples/dm6/geneA.txt -------------------------------------------------------------------------------- /public/examples/dm6/geneB.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/inutano/chip-atlas/HEAD/public/examples/dm6/geneB.txt -------------------------------------------------------------------------------- /public/examples/dm6/motifA.txt: -------------------------------------------------------------------------------- 1 | TRTTTACTTW 2 | -------------------------------------------------------------------------------- /public/examples/dm6/motifB.txt: -------------------------------------------------------------------------------- 1 | TRTTTGCTGA 2 | -------------------------------------------------------------------------------- /public/examples/hg19/bedA.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/inutano/chip-atlas/HEAD/public/examples/hg19/bedA.txt -------------------------------------------------------------------------------- /public/examples/hg19/bedB.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/inutano/chip-atlas/HEAD/public/examples/hg19/bedB.txt -------------------------------------------------------------------------------- /public/examples/hg19/countA.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/inutano/chip-atlas/HEAD/public/examples/hg19/countA.txt -------------------------------------------------------------------------------- /public/examples/hg19/geneA.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/inutano/chip-atlas/HEAD/public/examples/hg19/geneA.txt -------------------------------------------------------------------------------- /public/examples/hg19/geneB.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/inutano/chip-atlas/HEAD/public/examples/hg19/geneB.txt -------------------------------------------------------------------------------- /public/examples/hg19/motifA.txt: -------------------------------------------------------------------------------- 1 | TRTTTACTTW 2 | -------------------------------------------------------------------------------- /public/examples/hg19/motifB.txt: -------------------------------------------------------------------------------- 1 | TRTTTGCTGA 2 | -------------------------------------------------------------------------------- /public/examples/hg38/bedA.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/inutano/chip-atlas/HEAD/public/examples/hg38/bedA.txt -------------------------------------------------------------------------------- /public/examples/hg38/bedB.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/inutano/chip-atlas/HEAD/public/examples/hg38/bedB.txt -------------------------------------------------------------------------------- /public/examples/hg38/countA.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/inutano/chip-atlas/HEAD/public/examples/hg38/countA.txt -------------------------------------------------------------------------------- /public/examples/hg38/geneA.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/inutano/chip-atlas/HEAD/public/examples/hg38/geneA.txt -------------------------------------------------------------------------------- /public/examples/hg38/geneB.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/inutano/chip-atlas/HEAD/public/examples/hg38/geneB.txt -------------------------------------------------------------------------------- /public/examples/hg38/motifA.txt: -------------------------------------------------------------------------------- 1 | TRTTTACTTW 2 | -------------------------------------------------------------------------------- /public/examples/hg38/motifB.txt: -------------------------------------------------------------------------------- 1 | TRTTTGCTGA 2 | -------------------------------------------------------------------------------- /public/examples/mm10/bedA.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/inutano/chip-atlas/HEAD/public/examples/mm10/bedA.txt -------------------------------------------------------------------------------- /public/examples/mm10/bedB.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/inutano/chip-atlas/HEAD/public/examples/mm10/bedB.txt -------------------------------------------------------------------------------- /public/examples/mm10/countA.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/inutano/chip-atlas/HEAD/public/examples/mm10/countA.txt -------------------------------------------------------------------------------- /public/examples/mm10/geneA.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/inutano/chip-atlas/HEAD/public/examples/mm10/geneA.txt -------------------------------------------------------------------------------- /public/examples/mm10/geneB.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/inutano/chip-atlas/HEAD/public/examples/mm10/geneB.txt -------------------------------------------------------------------------------- /public/examples/mm10/motifA.txt: -------------------------------------------------------------------------------- 1 | TRTTTACTTW 2 | -------------------------------------------------------------------------------- /public/examples/mm10/motifB.txt: -------------------------------------------------------------------------------- 1 | TRTTTGCTGA 2 | -------------------------------------------------------------------------------- /public/examples/mm9/bedA.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/inutano/chip-atlas/HEAD/public/examples/mm9/bedA.txt -------------------------------------------------------------------------------- /public/examples/mm9/bedB.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/inutano/chip-atlas/HEAD/public/examples/mm9/bedB.txt -------------------------------------------------------------------------------- /public/examples/mm9/countA.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/inutano/chip-atlas/HEAD/public/examples/mm9/countA.txt -------------------------------------------------------------------------------- /public/examples/mm9/geneA.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/inutano/chip-atlas/HEAD/public/examples/mm9/geneA.txt -------------------------------------------------------------------------------- /public/examples/mm9/geneB.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/inutano/chip-atlas/HEAD/public/examples/mm9/geneB.txt -------------------------------------------------------------------------------- /public/examples/mm9/motifA.txt: -------------------------------------------------------------------------------- 1 | TRTTTACTTW 2 | -------------------------------------------------------------------------------- /public/examples/mm9/motifB.txt: -------------------------------------------------------------------------------- 1 | TRTTTGCTGA 2 | -------------------------------------------------------------------------------- /public/examples/rn6/bedA.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/inutano/chip-atlas/HEAD/public/examples/rn6/bedA.txt -------------------------------------------------------------------------------- /public/examples/rn6/bedB.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/inutano/chip-atlas/HEAD/public/examples/rn6/bedB.txt -------------------------------------------------------------------------------- /public/examples/rn6/countA.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/inutano/chip-atlas/HEAD/public/examples/rn6/countA.txt -------------------------------------------------------------------------------- /public/examples/rn6/geneA.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/inutano/chip-atlas/HEAD/public/examples/rn6/geneA.txt -------------------------------------------------------------------------------- /public/examples/rn6/geneB.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/inutano/chip-atlas/HEAD/public/examples/rn6/geneB.txt -------------------------------------------------------------------------------- /public/examples/rn6/motifA.txt: -------------------------------------------------------------------------------- 1 | TRTTTACTTW 2 | -------------------------------------------------------------------------------- /public/examples/rn6/motifB.txt: -------------------------------------------------------------------------------- 1 | TRTTTGCTGA 2 | -------------------------------------------------------------------------------- /public/examples/sacCer3/bedA.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/inutano/chip-atlas/HEAD/public/examples/sacCer3/bedA.txt -------------------------------------------------------------------------------- /public/examples/sacCer3/bedB.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/inutano/chip-atlas/HEAD/public/examples/sacCer3/bedB.txt -------------------------------------------------------------------------------- /public/examples/sacCer3/countA.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/inutano/chip-atlas/HEAD/public/examples/sacCer3/countA.txt -------------------------------------------------------------------------------- /public/examples/sacCer3/geneA.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/inutano/chip-atlas/HEAD/public/examples/sacCer3/geneA.txt -------------------------------------------------------------------------------- /public/examples/sacCer3/geneB.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/inutano/chip-atlas/HEAD/public/examples/sacCer3/geneB.txt -------------------------------------------------------------------------------- /public/examples/sacCer3/motifA.txt: -------------------------------------------------------------------------------- 1 | TRTTTACTTW 2 | -------------------------------------------------------------------------------- /public/examples/sacCer3/motifB.txt: -------------------------------------------------------------------------------- 1 | TRTTTGCTGA 2 | -------------------------------------------------------------------------------- /public/images/logo/chiba_uni_logo.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/inutano/chip-atlas/HEAD/public/images/logo/chiba_uni_logo.png -------------------------------------------------------------------------------- /public/images/logo/dbcls_logo.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/inutano/chip-atlas/HEAD/public/images/logo/dbcls_logo.png -------------------------------------------------------------------------------- /public/images/logo/ddbj_logo.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/inutano/chip-atlas/HEAD/public/images/logo/ddbj_logo.png -------------------------------------------------------------------------------- /public/images/logo/jst_logo.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/inutano/chip-atlas/HEAD/public/images/logo/jst_logo.png -------------------------------------------------------------------------------- /public/images/logo/ku_logo.jpg: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/inutano/chip-atlas/HEAD/public/images/logo/ku_logo.jpg -------------------------------------------------------------------------------- /public/images/logo/kumamoto_uni_logo.jpg: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/inutano/chip-atlas/HEAD/public/images/logo/kumamoto_uni_logo.jpg -------------------------------------------------------------------------------- /public/images/logo/kyoto_uni_logo.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/inutano/chip-atlas/HEAD/public/images/logo/kyoto_uni_logo.png -------------------------------------------------------------------------------- /public/images/logo/nbdc_logo.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/inutano/chip-atlas/HEAD/public/images/logo/nbdc_logo.png -------------------------------------------------------------------------------- /public/js/bootstrap.min.js: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/inutano/chip-atlas/HEAD/public/js/bootstrap.min.js -------------------------------------------------------------------------------- /public/js/ie10-viewport-bug-workaround.js: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/inutano/chip-atlas/HEAD/public/js/ie10-viewport-bug-workaround.js -------------------------------------------------------------------------------- /public/js/jquery.flexselect.js: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/inutano/chip-atlas/HEAD/public/js/jquery.flexselect.js -------------------------------------------------------------------------------- /public/js/jquery.min.js: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/inutano/chip-atlas/HEAD/public/js/jquery.min.js -------------------------------------------------------------------------------- /public/js/liquidmetal.js: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/inutano/chip-atlas/HEAD/public/js/liquidmetal.js -------------------------------------------------------------------------------- /public/js/pj/colo.js: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/inutano/chip-atlas/HEAD/public/js/pj/colo.js -------------------------------------------------------------------------------- /public/js/pj/diff_analysis.js: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/inutano/chip-atlas/HEAD/public/js/pj/diff_analysis.js -------------------------------------------------------------------------------- /public/js/pj/diff_analysis_result.js: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/inutano/chip-atlas/HEAD/public/js/pj/diff_analysis_result.js -------------------------------------------------------------------------------- /public/js/pj/enrichment_analysis.js: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/inutano/chip-atlas/HEAD/public/js/pj/enrichment_analysis.js -------------------------------------------------------------------------------- /public/js/pj/enrichment_analysis_result.js: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/inutano/chip-atlas/HEAD/public/js/pj/enrichment_analysis_result.js -------------------------------------------------------------------------------- /public/js/pj/experiment.js: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/inutano/chip-atlas/HEAD/public/js/pj/experiment.js -------------------------------------------------------------------------------- /public/js/pj/peak_browser.js: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/inutano/chip-atlas/HEAD/public/js/pj/peak_browser.js -------------------------------------------------------------------------------- /public/js/pj/pj.js: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/inutano/chip-atlas/HEAD/public/js/pj/pj.js -------------------------------------------------------------------------------- /public/js/pj/search.js: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/inutano/chip-atlas/HEAD/public/js/pj/search.js -------------------------------------------------------------------------------- /public/js/pj/target_genes.js: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/inutano/chip-atlas/HEAD/public/js/pj/target_genes.js -------------------------------------------------------------------------------- /public/js/typeahead.bundle.js: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/inutano/chip-atlas/HEAD/public/js/typeahead.bundle.js -------------------------------------------------------------------------------- /public/robots.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/inutano/chip-atlas/HEAD/public/robots.txt -------------------------------------------------------------------------------- /public/tables/exp2run.json: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/inutano/chip-atlas/HEAD/public/tables/exp2run.json -------------------------------------------------------------------------------- /public/tables/lineNum.tsv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/inutano/chip-atlas/HEAD/public/tables/lineNum.tsv -------------------------------------------------------------------------------- /public/webfonts/fa-brands-400.ttf: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/inutano/chip-atlas/HEAD/public/webfonts/fa-brands-400.ttf -------------------------------------------------------------------------------- /public/webfonts/fa-brands-400.woff2: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/inutano/chip-atlas/HEAD/public/webfonts/fa-brands-400.woff2 -------------------------------------------------------------------------------- /public/webfonts/fa-regular-400.ttf: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/inutano/chip-atlas/HEAD/public/webfonts/fa-regular-400.ttf -------------------------------------------------------------------------------- /public/webfonts/fa-regular-400.woff2: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/inutano/chip-atlas/HEAD/public/webfonts/fa-regular-400.woff2 -------------------------------------------------------------------------------- /public/webfonts/fa-solid-900.ttf: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/inutano/chip-atlas/HEAD/public/webfonts/fa-solid-900.ttf -------------------------------------------------------------------------------- /public/webfonts/fa-solid-900.woff2: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/inutano/chip-atlas/HEAD/public/webfonts/fa-solid-900.woff2 -------------------------------------------------------------------------------- /public/webfonts/fa-v4compatibility.ttf: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/inutano/chip-atlas/HEAD/public/webfonts/fa-v4compatibility.ttf -------------------------------------------------------------------------------- /public/webfonts/fa-v4compatibility.woff2: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/inutano/chip-atlas/HEAD/public/webfonts/fa-v4compatibility.woff2 -------------------------------------------------------------------------------- /rdf/README.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/inutano/chip-atlas/HEAD/rdf/README.md -------------------------------------------------------------------------------- /rdf/bin/bed2ttl: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/inutano/chip-atlas/HEAD/rdf/bin/bed2ttl -------------------------------------------------------------------------------- /rdf/bin/chr2genbank: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/inutano/chip-atlas/HEAD/rdf/bin/chr2genbank -------------------------------------------------------------------------------- /rdf/bin/rdfize_colo.awk: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/inutano/chip-atlas/HEAD/rdf/bin/rdfize_colo.awk -------------------------------------------------------------------------------- /rdf/bin/rdfize_target_genes.awk: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/inutano/chip-atlas/HEAD/rdf/bin/rdfize_target_genes.awk -------------------------------------------------------------------------------- /rdf/generate-rdf: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/inutano/chip-atlas/HEAD/rdf/generate-rdf -------------------------------------------------------------------------------- /rdf/images/chipatlas_analysis_rdf.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/inutano/chip-atlas/HEAD/rdf/images/chipatlas_analysis_rdf.png -------------------------------------------------------------------------------- /rdf/images/chipatlas_bindingsites_rdf.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/inutano/chip-atlas/HEAD/rdf/images/chipatlas_bindingsites_rdf.png -------------------------------------------------------------------------------- /rdf/ontology/cao.ttl: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/inutano/chip-atlas/HEAD/rdf/ontology/cao.ttl -------------------------------------------------------------------------------- /rdf/reference/GCF_000001215.2_Release_5_assembly_report.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/inutano/chip-atlas/HEAD/rdf/reference/GCF_000001215.2_Release_5_assembly_report.txt -------------------------------------------------------------------------------- /rdf/reference/GCF_000001635.18_MGSCv37_assembly_report.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/inutano/chip-atlas/HEAD/rdf/reference/GCF_000001635.18_MGSCv37_assembly_report.txt -------------------------------------------------------------------------------- /rdf/reference/GCF_000001895.5_Rnor_6.0_assembly_report.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/inutano/chip-atlas/HEAD/rdf/reference/GCF_000001895.5_Rnor_6.0_assembly_report.txt -------------------------------------------------------------------------------- /rdf/reference/GCF_000002985.5_WBcel215_assembly_report.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/inutano/chip-atlas/HEAD/rdf/reference/GCF_000002985.5_WBcel215_assembly_report.txt -------------------------------------------------------------------------------- /rdf/reference/GCF_000146045.2_R64_assembly_report.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/inutano/chip-atlas/HEAD/rdf/reference/GCF_000146045.2_R64_assembly_report.txt -------------------------------------------------------------------------------- /script/diff-analysis/diff_analysis_for_ChIP_ATAC_DNase.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/inutano/chip-atlas/HEAD/script/diff-analysis/diff_analysis_for_ChIP_ATAC_DNase.sh -------------------------------------------------------------------------------- /script/enrichment-analysis/Dockerfile: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/inutano/chip-atlas/HEAD/script/enrichment-analysis/Dockerfile -------------------------------------------------------------------------------- /script/enrichment-analysis/bedToBoundProteins.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/inutano/chip-atlas/HEAD/script/enrichment-analysis/bedToBoundProteins.sh -------------------------------------------------------------------------------- /script/enrichment-analysis/btbpToHtml.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/inutano/chip-atlas/HEAD/script/enrichment-analysis/btbpToHtml.txt -------------------------------------------------------------------------------- /script/enrichment-analysis/docker-compose.yml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/inutano/chip-atlas/HEAD/script/enrichment-analysis/docker-compose.yml -------------------------------------------------------------------------------- /script/enrichment-analysis/enrichment-analysis.cwl: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/inutano/chip-atlas/HEAD/script/enrichment-analysis/enrichment-analysis.cwl -------------------------------------------------------------------------------- /script/enrichment-analysis/enrichment-analysis.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/inutano/chip-atlas/HEAD/script/enrichment-analysis/enrichment-analysis.sh -------------------------------------------------------------------------------- /script/enrichment-analysis/geneList_A.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/inutano/chip-atlas/HEAD/script/enrichment-analysis/geneList_A.txt -------------------------------------------------------------------------------- /script/enrichment-analysis/geneList_B.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/inutano/chip-atlas/HEAD/script/enrichment-analysis/geneList_B.txt -------------------------------------------------------------------------------- /script/enrichment-analysis/job.params.json: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/inutano/chip-atlas/HEAD/script/enrichment-analysis/job.params.json -------------------------------------------------------------------------------- /script/enrichment-analysis/job.reference.json: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/inutano/chip-atlas/HEAD/script/enrichment-analysis/job.reference.json -------------------------------------------------------------------------------- /script/enrichment-analysis/job.yml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/inutano/chip-atlas/HEAD/script/enrichment-analysis/job.yml -------------------------------------------------------------------------------- /script/enrichment-analysis/test.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/inutano/chip-atlas/HEAD/script/enrichment-analysis/test.sh -------------------------------------------------------------------------------- /script/launch-instance/README.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/inutano/chip-atlas/HEAD/script/launch-instance/README.md -------------------------------------------------------------------------------- /script/launch-instance/launch-chip-atlas.conf.example: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/inutano/chip-atlas/HEAD/script/launch-instance/launch-chip-atlas.conf.example -------------------------------------------------------------------------------- /script/launch-instance/launch-chip-atlas.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/inutano/chip-atlas/HEAD/script/launch-instance/launch-chip-atlas.sh -------------------------------------------------------------------------------- /script/sapporo-enrichment-analysis/docker-compose.yml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/inutano/chip-atlas/HEAD/script/sapporo-enrichment-analysis/docker-compose.yml -------------------------------------------------------------------------------- /script/sapporo-enrichment-analysis/download-references.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/inutano/chip-atlas/HEAD/script/sapporo-enrichment-analysis/download-references.sh -------------------------------------------------------------------------------- /script/sapporo-enrichment-analysis/sapporo_config/run.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/inutano/chip-atlas/HEAD/script/sapporo-enrichment-analysis/sapporo_config/run.sh -------------------------------------------------------------------------------- /script/sapporo-enrichment-analysis/sapporo_config/service-info.json: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/inutano/chip-atlas/HEAD/script/sapporo-enrichment-analysis/sapporo_config/service-info.json -------------------------------------------------------------------------------- /script/systemctl/README.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/inutano/chip-atlas/HEAD/script/systemctl/README.md -------------------------------------------------------------------------------- /script/systemctl/chip-atlas: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/inutano/chip-atlas/HEAD/script/systemctl/chip-atlas -------------------------------------------------------------------------------- /script/update_2025/DA/DA: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/inutano/chip-atlas/HEAD/script/update_2025/DA/DA -------------------------------------------------------------------------------- /script/update_2025/DA/README.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/inutano/chip-atlas/HEAD/script/update_2025/DA/README.md -------------------------------------------------------------------------------- /script/update_2025/DA/edgeR.r: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/inutano/chip-atlas/HEAD/script/update_2025/DA/edgeR.r -------------------------------------------------------------------------------- /script/update_2025/DA/help.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/inutano/chip-atlas/HEAD/script/update_2025/DA/help.txt -------------------------------------------------------------------------------- /script/update_2025/DA/make_igv_session.awk: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/inutano/chip-atlas/HEAD/script/update_2025/DA/make_igv_session.awk -------------------------------------------------------------------------------- /script/update_2025/EA/EA: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/inutano/chip-atlas/HEAD/script/update_2025/EA/EA -------------------------------------------------------------------------------- /script/update_2025/EA/btbpToHtml.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/inutano/chip-atlas/HEAD/script/update_2025/EA/btbpToHtml.txt -------------------------------------------------------------------------------- /script/update_2025/EA/help.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/inutano/chip-atlas/HEAD/script/update_2025/EA/help.txt -------------------------------------------------------------------------------- /script/update_2025/EA/tsv_to_html.awk: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/inutano/chip-atlas/HEAD/script/update_2025/EA/tsv_to_html.awk -------------------------------------------------------------------------------- /script/update_2025/PAGE/GRNcreator: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/inutano/chip-atlas/HEAD/script/update_2025/PAGE/GRNcreator -------------------------------------------------------------------------------- /script/update_2025/PAGE/PAGE: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/inutano/chip-atlas/HEAD/script/update_2025/PAGE/PAGE -------------------------------------------------------------------------------- /script/update_2025/PAGE/btbpToHtml.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/inutano/chip-atlas/HEAD/script/update_2025/PAGE/btbpToHtml.txt -------------------------------------------------------------------------------- /script/update_2025/PAGE/help.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/inutano/chip-atlas/HEAD/script/update_2025/PAGE/help.txt -------------------------------------------------------------------------------- /script/update_2025/PAGE/page.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/inutano/chip-atlas/HEAD/script/update_2025/PAGE/page.R -------------------------------------------------------------------------------- /script/update_2025/PAGE/tsv_to_html.awk: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/inutano/chip-atlas/HEAD/script/update_2025/PAGE/tsv_to_html.awk -------------------------------------------------------------------------------- /test/count_functionality_test.js: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/inutano/chip-atlas/HEAD/test/count_functionality_test.js -------------------------------------------------------------------------------- /test/dmr/dataA.srx: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/inutano/chip-atlas/HEAD/test/dmr/dataA.srx -------------------------------------------------------------------------------- /test/dmr/dataB.srx: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/inutano/chip-atlas/HEAD/test/dmr/dataB.srx -------------------------------------------------------------------------------- /test/dmr/dmr.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/inutano/chip-atlas/HEAD/test/dmr/dmr.sh -------------------------------------------------------------------------------- /test/enrichment_test.html: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/inutano/chip-atlas/HEAD/test/enrichment_test.html -------------------------------------------------------------------------------- /unicorn.rb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/inutano/chip-atlas/HEAD/unicorn.rb -------------------------------------------------------------------------------- /views/_navigation.haml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/inutano/chip-atlas/HEAD/views/_navigation.haml -------------------------------------------------------------------------------- /views/about.haml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/inutano/chip-atlas/HEAD/views/about.haml -------------------------------------------------------------------------------- /views/colo.haml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/inutano/chip-atlas/HEAD/views/colo.haml -------------------------------------------------------------------------------- /views/diff_analysis.haml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/inutano/chip-atlas/HEAD/views/diff_analysis.haml -------------------------------------------------------------------------------- /views/diff_analysis_result.haml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/inutano/chip-atlas/HEAD/views/diff_analysis_result.haml -------------------------------------------------------------------------------- /views/enrichment_analysis.haml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/inutano/chip-atlas/HEAD/views/enrichment_analysis.haml -------------------------------------------------------------------------------- /views/enrichment_analysis_result.haml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/inutano/chip-atlas/HEAD/views/enrichment_analysis_result.haml -------------------------------------------------------------------------------- /views/experiment.haml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/inutano/chip-atlas/HEAD/views/experiment.haml -------------------------------------------------------------------------------- /views/footer.haml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/inutano/chip-atlas/HEAD/views/footer.haml -------------------------------------------------------------------------------- /views/not_found.haml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/inutano/chip-atlas/HEAD/views/not_found.haml -------------------------------------------------------------------------------- /views/peak_browser.haml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/inutano/chip-atlas/HEAD/views/peak_browser.haml -------------------------------------------------------------------------------- /views/publications.haml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/inutano/chip-atlas/HEAD/views/publications.haml -------------------------------------------------------------------------------- /views/publications.markdown: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/inutano/chip-atlas/HEAD/views/publications.markdown -------------------------------------------------------------------------------- /views/search.haml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/inutano/chip-atlas/HEAD/views/search.haml -------------------------------------------------------------------------------- /views/style.sass: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/inutano/chip-atlas/HEAD/views/style.sass -------------------------------------------------------------------------------- /views/target_genes.haml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/inutano/chip-atlas/HEAD/views/target_genes.haml -------------------------------------------------------------------------------- /views/updates.markdown: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/inutano/chip-atlas/HEAD/views/updates.markdown --------------------------------------------------------------------------------