InTAD

This package is for version 3.7 of Bioconductor; for the stable, up-to-date release version, see InTAD.

Search for correlation between epigenetic signals and gene expression in TADs


Bioconductor version: 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 (version "3.5") and enter:


if (!require("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")
Correlation of epigenetic signals and genes in TADs HTML R Script
Reference Manual PDF
NEWS Text

Details

biocViews ChIPSeq, Epigenetics, GeneExpression, HiC, RNASeq, Sequencing, Software
Version 1.0.0
In Bioconductor since BioC 3.7 (R-3.5) (6 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
System Requirements
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Suggests testthat, BiocStyle, knitr, rmarkdown
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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 https://bioconductor.org/packages/InTAD/
Package Downloads Report Download Stats
Old Source Packages for BioC 3.7 Source Archive