FitHiC

DOI: 10.18129/B9.bioc.FitHiC    

This package is for version 3.8 of Bioconductor; for the stable, up-to-date release version, see FitHiC.

Confidence estimation for intra-chromosomal contact maps

Bioconductor version: 3.8

Fit-Hi-C is a tool for assigning statistical confidence estimates to intra-chromosomal contact maps produced by genome-wide genome architecture assays such as Hi-C.

Author: Ferhat Ay [aut] (Python original, https://noble.gs.washington.edu/proj/fit-hi-c/), Timothy L. Bailey [aut], William S. Noble [aut], Ruyu Tan [aut, cre, trl] (R port)

Maintainer: Ruyu Tan <rut003 at ucsd.edu>

Installation

To install this package, start R (version "3.5") and enter:

if (!requireNamespace("BiocManager", quietly = TRUE))
    install.packages("BiocManager")
BiocManager::install("FitHiC")

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("FitHiC")

 

HTML	R Script	Vignette Title
PDF		Reference Manual
Text		NEWS

Details

biocViews	DNA3DStructure, Software
Version	1.8.0
In Bioconductor since	BioC 3.4 (R-3.3) (2.5 years)
License	GPL (>= 2)
Depends
Imports	data.table, fdrtool, grDevices, graphics, Rcpp, stats, utils
LinkingTo	Rcpp
Suggests	knitr, rmarkdown
SystemRequirements
Enhances
URL
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report

Package Archives

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

Source Package	FitHiC_1.8.0.tar.gz
Windows Binary	FitHiC_1.8.0.zip (32- & 64-bit)
Mac OS X 10.11 (El Capitan)	FitHiC_1.8.0.tgz
Source Repository	git clone https://git.bioconductor.org/packages/FitHiC
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/FitHiC
Package Short Url	http://bioconductor.org/packages/FitHiC/
Package Downloads Report	Download Stats