├── DESCRIPTION ├── EaCoN.Rproj ├── LICENSE ├── NAMESPACE ├── NEWS ├── R ├── BED_functions.R ├── EaCoN_functions.R ├── FACETS_hack.R ├── apt_cytoscan_process.R ├── apt_oncoscan_process.R ├── apt_snp6_process.R ├── germline_functions.R ├── mini_functions.R ├── plot_functions.R ├── renorm_functions.R └── wes_process.R ├── README.md ├── data ├── GRCh37-lite.rda ├── datalist ├── hg17.rda ├── hg18.rda ├── hg19.rda ├── hg38.rda ├── hs37d5.rda ├── mm10.rda ├── mm7.rda ├── mm8.rda ├── mm9.rda ├── refGene_cl_hg18.rda ├── refGene_cl_hg19.rda ├── refGene_cl_hg38.rda ├── refGene_cl_hs37d5.rda ├── rn5.rda ├── rn6.rda ├── targetlist_270.rda └── targetlist_475.rda ├── inst └── extdata │ └── html_report.Rmd └── man ├── ASCN.ASCAT.Rd ├── ASCN.FACETS.Rd ├── ASCN.SEQUENZA.Rd ├── ASCN.ff.Batch.Rd ├── ASCN.ff.Rd ├── Annotate.Rd ├── Annotate.ff.Batch.Rd ├── Annotate.ff.Rd ├── BINpack.Maker.Rd ├── BedCheck.Rd ├── BedGC.chr.Rd ├── BedGC.fasta.Rd ├── CS.Process.Batch.Rd ├── CS.Process.Rd ├── EaCoN.set.bitmapType.Rd ├── GC.data.Rd ├── OS.Process.Batch.Rd ├── OS.Process.Rd ├── SNP6.Process.Batch.Rd ├── SNP6.Process.Rd ├── Segment.ASCAT.Rd ├── Segment.FACETS.Rd ├── Segment.SEQUENZA.Rd ├── Segment.ff.Batch.Rd ├── Segment.ff.Rd ├── WES.Bin.Batch.Rd ├── WES.Bin.Rd ├── WES.Normalize.Rd ├── WES.Normalize.ff.Batch.Rd ├── WES.Normalize.ff.Rd ├── gen.df.Rd └── targetlist.Rd /DESCRIPTION: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/gustaveroussy/EaCoN/HEAD/DESCRIPTION -------------------------------------------------------------------------------- /EaCoN.Rproj: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/gustaveroussy/EaCoN/HEAD/EaCoN.Rproj -------------------------------------------------------------------------------- /LICENSE: -------------------------------------------------------------------------------- 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