├── .devcontainer └── devcontainer.json ├── .editorconfig ├── .gitattributes ├── .github ├── .dockstore.yml ├── CONTRIBUTING.md ├── ISSUE_TEMPLATE │ ├── bug_report.yml │ ├── config.yml │ └── feature_request.yml ├── PULL_REQUEST_TEMPLATE.md └── workflows │ ├── awsfulltest.yml │ ├── awstest.yml │ ├── branch.yml │ ├── ci.yml │ ├── clean-up.yml │ ├── download_pipeline.yml │ ├── fix-linting.yml │ ├── linting.yml │ ├── linting_comment.yml │ └── release-announcements.yml ├── .gitignore ├── .gitpod.yml ├── .nf-core.yml ├── .pre-commit-config.yaml ├── .prettierignore ├── .prettierrc.yml ├── CHANGELOG.md ├── CITATIONS.md ├── CODE_OF_CONDUCT.md ├── LICENSE ├── README.md ├── assets ├── adaptivecard.json ├── differentialabundance_report.Rmd ├── email_template.html ├── email_template.txt ├── methods_description_template.yml ├── multiqc_config.yml ├── nf-core-differentialabundance_logo_light.png ├── nf-core_style.css ├── schema_input.json ├── sendmail_template.txt └── slackreport.json ├── conf ├── affy.config ├── base.config ├── igenomes.config ├── maxquant.config ├── modules.config ├── rnaseq.config ├── soft.config ├── test.config ├── test_affy.config ├── test_full.config ├── test_maxquant.config ├── test_nogtf.config └── test_soft.config ├── docs ├── README.md ├── images │ ├── markdown_report.png │ ├── nf-core-differentialabundance_logo_dark.png │ ├── nf-core-differentialabundance_logo_light.png │ ├── shinyngs_contrast_table.png │ ├── shinyngs_gene_plot.png │ ├── workflow.png │ └── workflow.svg ├── output.md └── usage.md ├── main.nf ├── modules.json ├── modules ├── local │ ├── filter_difftable.nf │ └── tabular_to_gsea_chip.nf └── nf-core │ ├── affy │ └── justrma │ │ ├── environment.yml │ │ ├── main.nf │ │ ├── meta.yml │ │ └── templates │ │ └── affy_justrma.R │ ├── atlasgeneannotationmanipulation │ └── gtf2featureannotation │ │ ├── environment.yml │ │ ├── main.nf │ │ └── meta.yml │ ├── custom │ ├── matrixfilter │ │ ├── environment.yml │ │ ├── main.nf │ │ ├── meta.yml │ │ └── templates │ │ │ └── matrixfilter.R │ ├── tabulartogseacls │ │ ├── environment.yml │ │ ├── main.nf │ │ └── meta.yml │ └── tabulartogseagct │ │ ├── environment.yml │ │ ├── main.nf │ │ └── meta.yml │ ├── deseq2 │ └── differential │ │ ├── environment.yml │ │ ├── main.nf │ │ ├── meta.yml │ │ └── templates │ │ └── deseq_de.R │ ├── geoquery │ └── getgeo │ │ ├── environment.yml │ │ ├── main.nf │ │ ├── meta.yml │ │ └── templates │ │ └── getgeo.R │ ├── gprofiler2 │ └── gost │ │ ├── environment.yml │ │ ├── main.nf │ │ ├── meta.yml │ │ └── templates │ │ └── gprofiler2_gost.R │ ├── gsea │ └── gsea │ │ ├── environment.yml │ │ ├── main.nf │ │ └── meta.yml │ ├── gunzip │ ├── environment.yml │ ├── main.nf │ └── meta.yml │ ├── limma │ └── differential │ │ ├── environment.yml │ │ ├── main.nf │ │ ├── meta.yml │ │ └── templates │ │ └── limma_de.R │ ├── proteus │ └── readproteingroups │ │ ├── environment.yml │ │ ├── main.nf │ │ ├── meta.yml │ │ └── templates │ │ └── proteus_readproteingroups.R │ ├── rmarkdownnotebook │ ├── environment.yml │ ├── main.nf │ ├── meta.yml │ └── parametrize.nf │ ├── shinyngs │ ├── app │ │ ├── environment.yml │ │ ├── main.nf │ │ ├── meta.yml │ │ └── tests │ │ │ ├── main.nf.test │ │ │ ├── main.nf.test.snap │ │ │ ├── nextflow.config │ │ │ └── tags.yml │ ├── staticdifferential │ │ ├── environment.yml │ │ ├── main.nf │ │ └── meta.yml │ ├── staticexploratory │ │ ├── environment.yml │ │ ├── main.nf │ │ ├── meta.yml │ │ └── tests │ │ │ ├── main.nf.test │ │ │ ├── main.nf.test.snap │ │ │ ├── nextflow.config │ │ │ ├── nextflow_html.conf │ │ │ ├── nextflow_specify_log.conf │ │ │ └── tags.yml │ └── validatefomcomponents │ │ ├── environment.yml │ │ ├── main.nf │ │ └── meta.yml │ ├── untar │ ├── environment.yml │ ├── main.nf │ └── meta.yml │ └── zip │ ├── environment.yml │ ├── main.nf │ └── meta.yml ├── nextflow.config ├── nextflow_schema.json ├── pyproject.toml ├── subworkflows ├── local │ └── utils_nfcore_differentialabundance_pipeline │ │ └── main.nf └── nf-core │ 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