epidecodeR
epidecodeR: a functional exploration tool for epigenetic and epitranscriptomic regulation
Bioconductor version: 3.23 · Package version: 1.20.0
Other Bioconductor versions
devel is the development version; release is the current stable one.
3.24 (devel), 3.23 (release)
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.
Installation
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("epidecodeR")Details
| Maintainer | Kandarp Joshi <kandarpbioinfo@gmail.com> |
| Author | Kandarp Joshi [aut, cre], Dan Ohtan Wang [aut] |
| License | GPL-3 |
| URL | https://github.com/kandarpRJ/epidecodeR, https://epidecoder.shinyapps.io/shinyapp |
| Bug Reports | https://github.com/kandarpRJ/epidecodeR/issues |
| Source branch | RELEASE_3_23 |
| Build report | Bioconductor build system, r-universe |
| biocViews | ChipOnChip, DifferentialExpression, Epigenetics, Epitranscriptomics, FunctionalGenomics, FunctionalPrediction, GeneExpression, GeneRegulation, HistoneModification, Software, SystemsBiology, Transcription, Transcriptomics |
| Package Short Url | https://bioconductor.org/packages/epidecodeR/ |
Citation
From within R, enter citation("epidecodeR"):
Kandarp Joshi, Dan Ohtan Wang. epidecodeR: epidecodeR: a functional exploration tool for epigenetic and epitranscriptomic regulation. doi:10.18129/B9.bioc.epidecodeR, R package version 1.20.0, https://bioconductor.org/packages/epidecodeR.
Generated from the package metadata; it may differ from the package's own citation.
Documentation
Download
Follow the installation instructions to use this package in your R session.
| Source package | epidecodeR_1.20.0.tar.gz |
| Windows binary (x86_64) | epidecodeR_1.20.0.zip |
| macOS binary (arm64) | epidecodeR_1.20.0.tgz |
| macOS binary (x86_64) | epidecodeR_1.20.0.tgz |
Dependencies
Depends: R (>= 3.1.0)
Imports: EnvStats, ggplot2, rtracklayer, GenomicRanges, IRanges, rstatix, ggpubr, methods, stats, utils, dplyr