Package: InTAD
Type: Package
Title: Search for correlation between epigenetic signals and gene
        expression in TADs
Version: 1.31.0
Author: Konstantin Okonechnikov, Serap Erkek, Lukas Chavez
Maintainer: Konstantin Okonechnikov <k.okonechnikov@gmail.com>
Description: 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.
License: GPL (>=2)
LazyData: TRUE
Depends: R (>= 3.5), methods, S4Vectors, IRanges, GenomicRanges,
        MultiAssayExperiment, SummarizedExperiment,stats
Imports:
        BiocGenerics,Biobase,rtracklayer,parallel,graphics,mclust,qvalue,
        ggplot2,utils,ggpubr
biocViews: Epigenetics, Sequencing, ChIPSeq, RNASeq, HiC,
        GeneExpression,ImmunoOncology
VignetteBuilder: knitr
Suggests: testthat, BiocStyle, knitr, rmarkdown
RoxygenNote: 6.0.1
Config/pak/sysreqs: cmake make libbz2-dev libicu-dev liblzma-dev
        libxml2-dev libssl-dev xz-utils zlib1g-dev
Repository: https://bioc.r-universe.dev
Date/Publication: 2025-10-29 14:44:46 UTC
RemoteUrl: https://github.com/bioc/InTAD
RemoteRef: HEAD
RemoteSha: c1355bb894aed5a12d6354b38784b73d1f986094
NeedsCompilation: no
Packaged: 2026-02-17 09:08:19 UTC; root
Built: R 4.6.0; ; 2026-02-17 09:10:29 UTC; unix
