├── .Rbuildignore ├── .github └── workflows │ └── R-CMD-check.yaml ├── DESCRIPTION ├── NAMESPACE ├── NEWS.md ├── R ├── eisa-package.R ├── exportToGtf.R ├── getFeatureRanges.R ├── getRegionsFromTxDb.R ├── getTx2Gene.R ├── plotEISA.R └── runEISA.R ├── README.md ├── _pkgdown.yml ├── inst ├── CITATION ├── extdata │ ├── Fig3abc_GSE33252_rawcounts_exonic.rds │ ├── Fig3abc_GSE33252_rawcounts_intronic.rds │ ├── gencode.v28.annotation.sub.gtf │ ├── hg19sub.sqlite │ ├── small_example.gtf │ ├── small_example_genome.fa │ ├── small_example_t2g.txt │ └── small_example_txome.fa ├── scripts │ └── generate_example_data.R └── www │ └── eisaR.png ├── man ├── eisaR-package.Rd ├── exportToGtf.Rd ├── getFeatureRanges.Rd ├── getRegionsFromTxDb.Rd ├── getTx2Gene.Rd ├── plotEISA.Rd └── runEISA.Rd ├── tests ├── testthat.R └── testthat │ ├── test_getIntronAndTxSeqs.R │ ├── test_getRegionsFromTxDb.R │ ├── test_plotEISA.R │ └── test_runEISA.R └── vignettes ├── eisaR.Rmd ├── refs.bib └── rna-velocity.Rmd 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