InTAD

DOI: 10.18129/B9.bioc.InTAD    

Search for correlation between epigenetic signals and gene expression in TADs

Bioconductor version: Release (3.13)

The package is focused on the detection of correlation between expressed genes and selected epigenomic signals (i.e. enhancers obtained from ChIP-seq data) either within topologically associated domains (TADs) or between chromatin contact loop anchors. Various parameters can be controlled to investigate the influence of external factors and visualization plots are available for each analysis step.

Author: Konstantin Okonechnikov, Serap Erkek, Lukas Chavez

Maintainer: Konstantin Okonechnikov <k.okonechnikov at gmail.com>

Installation

To install this package, start R (version "4.1") and enter:

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

BiocManager::install("InTAD")

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("InTAD")

 

HTML	R Script	Correlation of epigenetic signals and genes in TADs
PDF		Reference Manual
Text		NEWS

Details

biocViews	ChIPSeq, Epigenetics, GeneExpression, HiC, ImmunoOncology, RNASeq, Sequencing, Software
Version	1.12.0
In Bioconductor since	BioC 3.7 (R-3.5) (3.5 years)
License	GPL (>=2)
Depends	R (>= 3.5), methods, S4Vectors, IRanges, GenomicRanges, MultiAssayExperiment, SummarizedExperiment, stats
Imports	BiocGenerics, Biobase, rtracklayer, parallel, graphics, mclust, qvalue, ggplot2, utils, ggpubr
LinkingTo
Suggests	testthat, BiocStyle, knitr, rmarkdown
SystemRequirements
Enhances
URL
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	InTAD_1.12.0.tar.gz
Windows Binary	InTAD_1.12.0.zip
macOS 10.13 (High Sierra)	InTAD_1.12.0.tgz
Source Repository	git clone https://git.bioconductor.org/packages/InTAD
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/InTAD
Package Short Url	https://bioconductor.org/packages/InTAD/
Package Downloads Report	Download Stats