epidecodeR

DOI: 10.18129/B9.bioc.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 (3.14)

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 "4.1") and enter:

if (!requireNamespace("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

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

browseVignettes("epidecodeR")

 

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

Details

biocViews ChipOnChip, DifferentialExpression, Epigenetics, Epitranscriptomics, FunctionalGenomics, FunctionalPrediction, GeneExpression, GeneRegulation, HistoneModification, Software, SystemsBiology, Transcription, Transcriptomics
Version 1.1.3
In Bioconductor since BioC 3.13 (R-4.1) (< 6 months)
License GPL-3
Depends R (>= 3.1.0)
Imports EnvStats, ggplot2, rtracklayer, GenomicRanges, IRanges, rstatix, ggpubr, methods, stats, utils, dplyr
LinkingTo
Suggests knitr, rmarkdown
SystemRequirements
Enhances
URL https://github.com/kandarpRJ/epidecodeR https://epidecoder.shinyapps.io/shinyapp
BugReports https://github.com/kandarpRJ/epidecodeR/issues
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report  

Package Archives

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

Source Package epidecodeR_1.1.3.tar.gz
Windows Binary epidecodeR_1.1.3.zip
macOS 10.13 (High Sierra) epidecodeR_1.1.3.tgz
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

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