DOI: 10.18129/B9.bioc.TADCompare    

TADCompare: Identification and characterization of differential TADs

Bioconductor version: Release (3.14)

TADCompare is an R package designed to identify and characterize differential Topologically Associated Domains (TADs) between multiple Hi-C contact matrices. It contains functions for finding differential TADs between two datasets, finding differential TADs over time and identifying consensus TADs across multiple matrices. It takes all of the main types of HiC input and returns simple, comprehensive, easy to analyze results.

Author: Kellen Cresswell <cresswellkg at vcu.edu>, Mikhail Dozmorov <mikhail.dozmorov at vcuhealth.org>

Maintainer: Kellen Cresswell <cresswellkg at vcu.edu>

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HTML R Script Gene Ontology Enrichment Analysis
HTML R Script Input data formats
HTML R Script TAD comparison between two conditions
PDF   Reference Manual
Text   NEWS


biocViews Clustering, FeatureExtraction, HiC, Sequencing, Software
Version 1.4.0
In Bioconductor since BioC 3.12 (R-4.0) (1 year)
License MIT + file LICENSE
Depends R (>= 4.0)
Imports dplyr, PRIMME, cluster, Matrix, magrittr, HiCcompare, ggplot2, tidyr, ggpubr, RColorBrewer, reshape2, cowplot
Suggests BiocStyle, knitr, rmarkdown, microbenchmark, testthat, covr, pheatmap, rGREAT, SpectralTAD
URL https://github.com/dozmorovlab/TADCompare
BugReports https://github.com/dozmorovlab/TADCompare/issues
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Source Package TADCompare_1.4.0.tar.gz
Windows Binary TADCompare_1.4.0.zip
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Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/TADCompare
Package Short Url https://bioconductor.org/packages/TADCompare/
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