TADCompare
This is the development version of TADCompare; for the stable release version, see TADCompare.
TADCompare: Identification and characterization of differential TADs
Bioconductor version: Development (3.24)
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: Mikhail Dozmorov [aut, cre] 
, Kellen Cresswell [aut]
Maintainer: Mikhail Dozmorov <mikhail.dozmorov at gmail.com>
citation("TADCompare")):Mikhail Dozmorov, Kellen Cresswell. TADCompare: TADCompare: Identification and characterization of differential TADs. doi:10.18129/B9.bioc.TADCompare, R package version 1.23.5, https://bioconductor.org/packages/TADCompare.
Generated from the package metadata; it may differ from the package's own citation.
Installation
To install this package, start R (version "4.6") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
## The following initializes the development version of Bioconductor
BiocManager::install(version = "devel")
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")| Input data formats | HTML | R Script |
| Gene Ontology Enrichment Analysis | 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 | 1.23.5 |
| In Bioconductor since | BioC 3.12 (R-4.0) (6 years) |
| License | MIT + file LICENSE |
| Depends | R (>= 4.0) |
| Imports | dplyr, cluster, Matrix, magrittr, HiCcompare, ggplot2, tidyr, ggpubr, RColorBrewer, reshape2, cowplot |
| System Requirements | |
| URL | https://github.com/dozmorovlab/TADCompare |
| 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, r-universe |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | TADCompare_1.23.5.tar.gz |
| Windows Binary (x86_64) | TADCompare_1.23.5.zip (64-bit only) |
| macOS Binary (big-sur-x86_64) | TADCompare_1.23.5.tgz |
| macOS Binary (sonoma-arm64) | TADCompare_1.23.5.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 |