├── .gitignore ├── .travis.yml ├── DESCRIPTION ├── NAMESPACE ├── R ├── RcppExports.R ├── argparsing.R ├── avgStateProfile.R ├── bamtab.R ├── colors.R ├── counts.R ├── getcounts.R ├── html.R ├── main.R ├── model.R ├── myheat.R ├── normalization.R ├── normalizecounts.R ├── regions.R ├── report.R └── segment.R ├── README.md ├── inst ├── examples │ ├── cliExamples.Rmd │ └── examples.R ├── extdata │ ├── 5s_model.txt │ ├── 5s_segmentation.bed │ ├── H3K36me3.bam │ ├── H3K36me3.bam.bai │ ├── H3K4me3.bam │ ├── H3K4me3.bam.bai │ ├── H3K9me3.bam │ ├── H3K9me3.bam.bai │ ├── contigs.bed │ ├── counts.txt │ ├── genes.bed │ └── uflow_minimal.Rdata └── manual.html ├── man ├── epicseg.Rd ├── getcounts.Rd ├── normalizecounts.Rd ├── refineRegions.Rd ├── report.Rd └── segment.Rd ├── src ├── Makevars ├── RcppExports.cpp ├── array.h ├── clist.h ├── misc.cpp ├── normalization.cpp ├── segments.cpp └── tabbing.h └── tests ├── testthat.R └── testthat ├── test-RI.R ├── test-_CLI.R ├── test-normalization.R ├── 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