This package is for version 3.13 of Bioconductor; for the stable, up-to-date release version, see TADCompare.
Bioconductor version: 3.13
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>
Citation (from within R,
enter citation("TADCompare")
):
To install this package, start R (version "4.1") and enter:
if (!requireNamespace("BiocManager", quietly = TRUE)) install.packages("BiocManager") BiocManager::install("TADCompare")
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:
browseVignettes("TADCompare")
HTML | R Script | Gene Ontology Enrichment Analysis |
HTML | R Script | Input data formats |
HTML | R Script | TAD comparison between two conditions |
Reference Manual | ||
Text | NEWS | |
Text | LICENSE |
biocViews | Clustering, FeatureExtraction, HiC, Sequencing, Software |
Version | 1.2.0 |
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 |
LinkingTo | |
Suggests | BiocStyle, knitr, rmarkdown, microbenchmark, testthat, covr, pheatmap, rGREAT, SpectralTAD |
SystemRequirements | |
Enhances | |
URL | https://github.com/dozmorovlab/TADCompare |
BugReports | https://github.com/dozmorovlab/TADCompare/issues |
Depends On Me | |
Imports Me | |
Suggests Me | |
Links To Me | |
Build Report |
Follow Installation instructions to use this package in your R session.
Source Package | TADCompare_1.2.0.tar.gz |
Windows Binary | TADCompare_1.2.0.zip |
macOS 10.13 (High Sierra) | TADCompare_1.2.0.tgz |
Source Repository | git clone https://git.bioconductor.org/packages/TADCompare |
Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/TADCompare |
Package Short Url | https://bioconductor.org/packages/TADCompare/ |
Package Downloads Report | Download Stats |
Documentation »
Bioconductor
R / CRAN packages and documentation
Support »
Please read the posting guide. Post questions about Bioconductor to one of the following locations: