├── .gitignore ├── DESCRIPTION ├── LICENSE ├── NAMESPACE ├── NEWS.md ├── R ├── CMScaller.R ├── CMSgsa.R ├── cohensKappa.R ├── corCosine.R ├── data.R ├── ematAdjust.R ├── fromTo.R ├── ntp.R ├── ntpMakeTemplates.R ├── plotPC.R ├── replaceGeneId.R ├── rutils.R ├── subBoxplot.R ├── subCamera.R ├── subDEG.R ├── subHeatmap.R ├── subMA.R ├── subMDS.R ├── subPCA.R ├── subPairs.R ├── subSetNA.R ├── subVolcano.R ├── sysdata.rda └── voomTransform.R ├── README.md ├── data ├── anno.orgHs.rda ├── crcTCGAsubset.rda ├── geneSets.CMS.rda ├── geneSets.CRC.rda ├── geneSets.reactome.rda ├── templates.CMS.rda ├── templates.CRIS.rda └── templates.MSI.rda ├── inst ├── CITATION └── doc │ ├── CMScaller.R │ ├── CMScaller.Rmd │ ├── CMScaller.html │ └── CMScaller.pdf ├── man ├── CMScaller.Rd ├── CMSgsa.Rd ├── anno.orgHs.Rd ├── cohensKappa.Rd ├── corCosine.Rd ├── crcTCGAsubset.Rd ├── ematAdjust.Rd ├── fromTo.Rd ├── geneSets.CMS.Rd ├── geneSets.CRC.Rd ├── geneSets.reactome.Rd ├── ntp.Rd ├── ntpMakeTemplates.Rd ├── replaceGeneId.Rd ├── subBoxplot.Rd ├── subCamera.Rd ├── subDEG.Rd ├── subHeatmap.Rd ├── subMA.Rd ├── subMDS.Rd ├── subPCA.Rd ├── subPairs.Rd ├── subSetNA.Rd ├── subVolcano.Rd ├── templates.CMS.Rd ├── templates.CRIS.Rd └── templates.MSI.Rd └── vignettes ├── CMScaller.Rmd ├── CMScaller.bib └── biomed-central /.gitignore: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/peterawe/CMScaller/HEAD/.gitignore -------------------------------------------------------------------------------- /DESCRIPTION: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/peterawe/CMScaller/HEAD/DESCRIPTION -------------------------------------------------------------------------------- /LICENSE: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/peterawe/CMScaller/HEAD/LICENSE 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