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Search for correlation between epigenetic signals and gene expression in TADs

Bioconductor version: Release (3.18)

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")):


To install this package, start R (version "4.3") and enter:

if (!require("BiocManager", quietly = TRUE))


For older versions of R, please refer to the appropriate Bioconductor release.


To view documentation for the version of this package installed in your system, start R and enter:

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


biocViews ChIPSeq, Epigenetics, GeneExpression, HiC, ImmunoOncology, RNASeq, Sequencing, Software
Version 1.22.0
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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Follow Installation instructions to use this package in your R session.

Source Package InTAD_1.22.0.tar.gz
Windows Binary InTAD_1.22.0.zip
macOS Binary (x86_64) InTAD_1.22.0.tgz
macOS Binary (arm64) InTAD_1.22.0.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/
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