TADCompare
This package is for version 3.12 of Bioconductor; for the stable, up-to-date release version, see TADCompare.
TADCompare: Identification and characterization of differential TADs
Bioconductor version: 3.12
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("TADCompare")):
Installation
To install this package, start R (version "4.0") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("TADCompare")
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("TADCompare")| Gene Ontology Enrichment Analysis | HTML | R Script |
| Input data formats | HTML | R Script |
| TAD comparison between two conditions | HTML | R Script |
| Reference Manual | ||
| NEWS | Text | |
| LICENSE | Text |
Details
| biocViews | Clustering, FeatureExtraction, HiC, Sequencing, Software |
| Version | 1.0.0 |
| In Bioconductor since | BioC 3.12 (R-4.0) (3.5 years) |
| License | MIT + file LICENSE |
| Depends | R (>= 4.0) |
| Imports | dplyr, PRIMME, cluster, Matrix, magrittr, HiCcompare, ggplot2, tidyr, ggpubr, RColorBrewer, reshape2, cowplot |
| System Requirements | |
| URL | |
| Bug Reports | https://github.com/dozmorovlab/TADCompare/issues |
See More
| Suggests | BiocStyle, knitr, rmarkdown, microbenchmark, testthat, covr, pheatmap, rGREAT, SpectralTAD |
| Linking To | |
| Enhances | |
| Depends On Me | |
| Imports Me | |
| Suggests Me | |
| Links To Me | |
| Build Report | Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | TADCompare_1.0.0.tar.gz |
| Windows Binary | TADCompare_1.0.0.zip |
| macOS 10.13 (High Sierra) | TADCompare_1.0.0.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/TADCompare |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/TADCompare |
| Bioc Package Browser | https://code.bioconductor.org/browse/TADCompare/ |
| Package Short Url | https://bioconductor.org/packages/TADCompare/ |
| Package Downloads Report | Download Stats |
| Old Source Packages for BioC 3.12 | Source Archive |