Package: epidecodeR
Type: Package
Title: epidecodeR: a functional exploration tool for epigenetic and
        epitranscriptomic regulation
Version: 1.16.0
Authors@R: c(person("Kandarp", "Joshi", email = "kandarpbioinfo@gmail.com",
                  role = c("aut", "cre")),
             person("Dan", "Ohtan Wang", email = "ohtan@riken.jp",
                  role = "aut"))
BugReports: https://github.com/kandarpRJ/epidecodeR/issues
URL: https://github.com/kandarpRJ/epidecodeR,
        https://epidecoder.shinyapps.io/shinyapp
Depends: R (>= 3.1.0)
Imports: EnvStats, ggplot2, rtracklayer, GenomicRanges, IRanges,
        rstatix, ggpubr, methods, stats, utils, dplyr
biocViews: DifferentialExpression, GeneRegulation, HistoneModification,
        FunctionalPrediction, Transcription, GeneExpression,
        Epitranscriptomics, Epigenetics, FunctionalGenomics,
        SystemsBiology, Transcriptomics, ChipOnChip
Description: epidecodeR is a package capable of analysing impact of degree of DNA/RNA epigenetic chemical modifications on dysregulation of genes or proteins. This package integrates chemical modification data generated from a host of epigenomic or epitranscriptomic techniques such as ChIP-seq, ATAC-seq, m6A-seq, etc. and dysregulated gene lists in the form of differential gene expression, ribosome occupancy or differential protein translation and identify impact of dysregulation of genes caused due to varying degrees of chemical modifications associated with the genes. epidecodeR generates cumulative distribution function (CDF) plots showing shifts in trend of overall log2FC between genes divided into groups based on the degree of modification associated with the genes. The tool also tests for significance of difference in log2FC between groups of genes.
License: GPL-3
Encoding: UTF-8
RoxygenNote: 7.1.1
Suggests: knitr, rmarkdown
VignetteBuilder: knitr
git_url: https://git.bioconductor.org/packages/epidecodeR
git_branch: RELEASE_3_21
git_last_commit: e774461
git_last_commit_date: 2025-04-15
Repository: Bioconductor 3.21
Date/Publication: 2025-04-15
NeedsCompilation: no
Packaged: 2025-04-16 00:28:14 UTC; biocbuild
Author: Kandarp Joshi [aut, cre],
  Dan Ohtan Wang [aut]
Maintainer: Kandarp Joshi <kandarpbioinfo@gmail.com>
Built: R 4.5.0; ; 2025-04-16 14:24:14 UTC; windows
