InTAD

DOI: 10.18129/B9.bioc.InTAD    

Search for correlation between epigenetic signals and gene expression in TADs

Bioconductor version: Release (3.7)

The package is focused on the detection of correlation between expressed genes and selected epigenomic signals i.e. enhancers obtained from ChIP-seq data within topologically associated domains (TADs). 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>

Citation (from within R, enter citation("InTAD")):

Installation

To install this package, start R and enter:

## try http:// if https:// URLs are not supported
source("https://bioconductor.org/biocLite.R")
biocLite("InTAD")

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, RNASeq, Sequencing, Software
Version 1.0.0
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_1.0.0.tar.gz
Windows Binary InTAD_1.0.0.zip
Mac OS X 10.11 (El Capitan) InTAD_1.0.0.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 http://bioconductor.org/packages/InTAD/
Package Downloads Report Download Stats

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