InTAD

This package is for version 3.14 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: 3.14

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>

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

Installation

To install this package, start R (version "4.1") 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, ImmunoOncology, RNASeq, Sequencing, Software
Version 1.14.0
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
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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_1.14.0.tar.gz
Windows Binary InTAD_1.14.0.zip
macOS 10.13 (High Sierra) InTAD_1.14.0.tgz
Source Repository git clone https://git.bioconductor.org/packages/InTAD
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/InTAD
Bioc Package Browser https://code.bioconductor.org/browse/InTAD/
Package Short Url https://bioconductor.org/packages/InTAD/
Package Downloads Report Download Stats
Old Source Packages for BioC 3.14 Source Archive