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This is the development version of epidecodeR; for the stable release version, see epidecodeR.

epidecodeR: a functional exploration tool for epigenetic and epitranscriptomic regulation

Bioconductor version: Development (3.20)

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.

Author: Kandarp Joshi [aut, cre], Dan Ohtan Wang [aut]

Maintainer: Kandarp Joshi <kandarpbioinfo at>

Citation (from within R, enter citation("epidecodeR")):


To install this package, start R (version "4.4") and enter:

if (!require("BiocManager", quietly = TRUE))

# The following initializes usage of Bioc devel


For older versions of R, please refer to the appropriate Bioconductor release.


To view documentation for the version of this package installed in your system, start R and enter:

epidecodeR: a functional exploration tool for epigenetic and epitranscriptomic regulation HTML R Script
Reference Manual PDF


biocViews ChipOnChip, DifferentialExpression, Epigenetics, Epitranscriptomics, FunctionalGenomics, FunctionalPrediction, GeneExpression, GeneRegulation, HistoneModification, Software, SystemsBiology, Transcription, Transcriptomics
Version 1.13.0
In Bioconductor since BioC 3.13 (R-4.1) (3 years)
License GPL-3
Depends R (>= 3.1.0)
Imports EnvStats, ggplot2, rtracklayer, GenomicRanges, IRanges, rstatix, ggpubr, methods, stats, utils, dplyr
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Source Package epidecodeR_1.13.0.tar.gz
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