├── .gitignore ├── GSE91061_BMS038109Sample.hg19KnownGene.raw.csv.gz ├── README.md ├── batch_correlated_condition.R ├── batch_sim.csv ├── batch_sim_result.png ├── preNivolumabOnNivolumab.Rmd ├── preNivolumabOnNivolumab.html ├── preNivolumabOnNivolumab.knit.md └── preNivolumabOnNivolumab_files ├── bootstrap-3.3.5 ├── css │ ├── bootstrap-theme.css │ ├── bootstrap-theme.css.map │ ├── bootstrap-theme.min.css │ ├── bootstrap.css │ ├── bootstrap.css.map │ ├── bootstrap.min.css │ ├── cerulean.min.css │ ├── cosmo.min.css │ ├── darkly.min.css │ ├── flatly.min.css │ ├── fonts │ │ ├── Lato.ttf │ │ ├── LatoBold.ttf │ │ ├── LatoItalic.ttf │ │ ├── NewsCycle.ttf │ │ ├── NewsCycleBold.ttf │ │ ├── OpenSans.ttf │ │ ├── OpenSansBold.ttf │ │ ├── OpenSansBoldItalic.ttf │ │ ├── OpenSansItalic.ttf │ │ ├── OpenSansLight.ttf │ │ ├── OpenSansLightItalic.ttf │ │ ├── Raleway.ttf │ │ ├── RalewayBold.ttf │ │ ├── Roboto.ttf │ │ ├── RobotoBold.ttf │ │ ├── RobotoLight.ttf │ │ ├── RobotoMedium.ttf │ │ ├── SourceSansPro.ttf │ │ ├── SourceSansProBold.ttf │ │ ├── SourceSansProItalic.ttf │ │ ├── SourceSansProLight.ttf │ │ └── Ubuntu.ttf │ ├── journal.min.css │ ├── lumen.min.css │ ├── paper.min.css │ ├── readable.min.css │ ├── sandstone.min.css │ ├── simplex.min.css │ ├── spacelab.min.css │ ├── united.min.css │ └── yeti.min.css ├── fonts │ ├── glyphicons-halflings-regular.eot │ ├── glyphicons-halflings-regular.svg │ ├── glyphicons-halflings-regular.ttf │ ├── glyphicons-halflings-regular.woff │ └── glyphicons-halflings-regular.woff2 ├── js │ ├── bootstrap.js │ ├── bootstrap.min.js │ └── npm.js └── shim │ ├── html5shiv.min.js │ └── respond.min.js ├── figure-html ├── edgerDESeq2Compare-1.png ├── edgerDESeq2pvalues-1.png ├── maplot-1.png ├── pca1-1.png ├── pca2-1.png ├── pca3-1.png ├── pca3-2.png ├── pcaForOutlier-1.png └── pcaForOutlier-2.png ├── header-attrs-2.11 └── header-attrs.js ├── highlightjs-9.12.0 ├── default.css ├── highlight.js └── textmate.css ├── jquery-3.6.0 ├── jquery-3.6.0.js 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