DOI: 10.18129/B9.bioc.InTAD    

This is the development version of InTAD; for the stable release version, see InTAD.

Search for correlation between epigenetic signals and gene expression in TADs

Bioconductor version: Development (3.15)

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>

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


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biocViews ChIPSeq, Epigenetics, GeneExpression, HiC, ImmunoOncology, RNASeq, Sequencing, Software
Version 1.15.0
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
Suggests testthat, BiocStyle, knitr, rmarkdown
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