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>

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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
Suggests knitr, rmarkdown
URL https://github.com/kandarpRJ/epidecodeR https://epidecoder.shinyapps.io/shinyapp
BugReports https://github.com/kandarpRJ/epidecodeR/issues
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Source Package epidecodeR_1.1.3.tar.gz
Windows Binary epidecodeR_1.1.3.zip (32- & 64-bit)
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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/
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