Package: epidecodeR
Type: Package
Title: epidecodeR: a functional exploration tool for epigenetic and
        epitranscriptomic regulation
Version: 1.18.0
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
Config/pak/sysreqs: cmake make libbz2-dev libicu-dev liblzma-dev
        libxml2-dev libssl-dev xz-utils zlib1g-dev
Repository: https://bioc-release.r-universe.dev
Date/Publication: 2025-10-29 15:07:52 UTC
RemoteUrl: https://github.com/bioc/epidecodeR
RemoteRef: RELEASE_3_22
RemoteSha: df3fe88616f10268eda914392c68091dcc2d3642
NeedsCompilation: no
Packaged: 2025-11-11 14:16:41 UTC; root
Author: Kandarp Joshi [aut, cre],
  Dan Ohtan Wang [aut]
Maintainer: Kandarp Joshi <kandarpbioinfo@gmail.com>
Built: R 4.5.2; ; 2025-11-11 14:22:24 UTC; windows
