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Bioconductor - InTAD (development version)

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 (3.22)

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 "4.5") and enter:


if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

# The following initializes usage of Bioc devel
BiocManager::install(version='devel')

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 1.29.1 In Bioconductor since BioC 3.7 (R-3.5) (7 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 URL See More Package Archives

Follow Installation instructions to use this package in your R session.

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