HiTC

This is the released version of HiTC; for the devel version, see HiTC.

All versions

3.24 (devel), 3.23 (release), 3.22, 3.21, 3.20, 3.19, 3.18, 3.17, 3.16, 3.15, 3.14, 3.13, 3.12, 3.11, 3.10, 3.9, 3.8, 3.7, 3.6, 3.5, 3.4, 3.3, 3.2, 3.1, 3.0, 2.14, 2.13, 2.12, 2.11, 2.10

High Throughput Chromosome Conformation Capture analysis

Bioconductor version: Release (3.23)

The HiTC package was developed to explore high-throughput 'C' data such as 5C or Hi-C. Dedicated R classes as well as standard methods for quality controls, normalization, visualization, and further analysis are also provided.

Author: Nicolas Servant

Maintainer: Nicolas Servant <nicolas.servant at curie.fr>

Citation (from within R, enter citation("HiTC")):

Nicolas Servant. HiTC: High Throughput Chromosome Conformation Capture analysis. doi:10.18129/B9.bioc.HiTC, R package version 1.56.0, https://bioconductor.org/packages/HiTC.

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")

BiocManager::install("HiTC")

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("HiTC")

Hi-C data analysis using HiTC	PDF	R Script
Introduction to HiTC package	PDF	R Script
Reference Manual	PDF
NEWS	Text

Need some help? Ask on the Bioconductor Support site!

Details

biocViews	HiC, HighThroughputSequencing, Sequencing, Software
Version	1.56.0
In Bioconductor since	BioC 2.10 (R-2.15) (14.5 years)
License	Artistic-2.0
Depends	R (>= 2.15.0), methods, IRanges, GenomicRanges
Imports	Biostrings, graphics, grDevices, rtracklayer, RColorBrewer, Matrix, parallel, Seqinfo
System Requirements
URL

Suggests	BiocStyle, HiCDataHumanIMR90, BSgenome.Hsapiens.UCSC.hg18
Linking To
Enhances
Depends On Me
Imports Me
Suggests Me	adjclust, HiCDataHumanIMR90, HiCDCPlus
Links To Me
Build Report	Build Report, r-universe

Package Archives

Follow Installation instructions to use this package in your R session.

Source Package	HiTC_1.56.0.tar.gz
Windows Binary (x86_64)	HiTC_1.56.0.zip (64-bit only)
macOS Binary (big-sur-x86_64)	HiTC_1.56.0.tgz
macOS Binary (sonoma-arm64)	HiTC_1.56.0.tgz
Source Repository	git clone https://git.bioconductor.org/packages/HiTC
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/HiTC
Package Short Url	https://bioconductor.org/packages/HiTC/
Package Downloads Report	Download Stats