epidecodeR

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 (3.19)

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 gmail.com>

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

Installation

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


if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

# The following initializes usage of Bioc devel
BiocManager::install(version='devel')

BiocManager::install("epidecodeR")

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

Documentation


Reference Manual	PDF

Need some help? Ask on the Bioconductor Support site!

Details

biocViews	ChipOnChip, DifferentialExpression, Epigenetics, Epitranscriptomics, FunctionalGenomics, FunctionalPrediction, GeneExpression, GeneRegulation, HistoneModification, Software, SystemsBiology, Transcription, Transcriptomics
Version	1.11.0
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
System Requirements
URL	https://github.com/kandarpRJ/epidecodeR https://epidecoder.shinyapps.io/shinyapp
Bug Reports	https://github.com/kandarpRJ/epidecodeR/issues

Suggests	knitr, rmarkdown
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Build Report	Build Report

Package Archives

Follow Installation instructions to use this package in your R session.

Source Package
Windows Binary
macOS Binary (x86_64)
macOS Binary (arm64)
Source Repository	git clone https://git.bioconductor.org/packages/epidecodeR
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/epidecodeR
Package Short Url	https://bioconductor.org/packages/epidecodeR/
Package Downloads Report	Download Stats