epidecodeR
This package is for version 3.19 of Bioconductor; for the stable, up-to-date release version, see epidecodeR.
epidecodeR: a functional exploration tool for epigenetic and epitranscriptomic regulation
Bioconductor version: 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("epidecodeR")):
Installation
To install this package, start R (version "4.4") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
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")| epidecodeR: a functional exploration tool for epigenetic and epitranscriptomic regulation | HTML | R Script |
| Reference Manual |
Details
| biocViews | ChipOnChip, DifferentialExpression, Epigenetics, Epitranscriptomics, FunctionalGenomics, FunctionalPrediction, GeneExpression, GeneRegulation, HistoneModification, Software, SystemsBiology, Transcription, Transcriptomics |
| Version | 1.12.0 |
| In Bioconductor since | BioC 3.13 (R-4.1) (3.5 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 |
See More
| Suggests | knitr, rmarkdown |
| Linking To | |
| Enhances | |
| Depends On Me | |
| Imports Me | |
| Suggests Me | |
| Links To Me | |
| Build Report | Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | epidecodeR_1.12.0.tar.gz |
| Windows Binary (x86_64) | epidecodeR_1.12.0.zip |
| macOS Binary (x86_64) | epidecodeR_1.12.0.tgz |
| macOS Binary (arm64) | epidecodeR_1.12.0.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/epidecodeR |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/epidecodeR |
| Bioc Package Browser | https://code.bioconductor.org/browse/epidecodeR/ |
| Package Short Url | https://bioconductor.org/packages/epidecodeR/ |
| Package Downloads Report | Download Stats |