deltaCaptureC

DOI: 10.18129/B9.bioc.deltaCaptureC    

This package is for version 3.11 of Bioconductor; for the stable, up-to-date release version, see deltaCaptureC.

This Package Discovers Meso-scale Chromatin Remodeling from 3C Data

Bioconductor version: 3.11

This package discovers meso-scale chromatin remodelling from 3C data. 3C data is local in nature. It givens interaction counts between restriction enzyme digestion fragments and a preferred 'viewpoint' region. By binning this data and using permutation testing, this package can test whether there are statistically significant changes in the interaction counts between the data from two cell types or two treatments.

Author: Michael Shapiro [aut, cre]

Maintainer: Michael Shapiro <sifka at earthlink.net>

Installation

To install this package, start R (version "4.0") and enter:

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

BiocManager::install("deltaCaptureC")

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("deltaCaptureC")

 

HTML	R Script	Delta Capture-C
PDF		Reference Manual
Text		LICENSE

Details

biocViews	BiologicalQuestion, Software, StatisticalMethod
Version	1.2.0
In Bioconductor since	BioC 3.10 (R-3.6) (1 year)
License	MIT + file LICENSE
Depends	R (>= 3.6)
Imports	IRanges, GenomicRanges, SummarizedExperiment, ggplot2, DESeq2
LinkingTo
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	deltaCaptureC_1.2.0.tar.gz
Windows Binary	deltaCaptureC_1.2.0.zip
macOS 10.13 (High Sierra)	deltaCaptureC_1.2.0.tgz
Source Repository	git clone https://git.bioconductor.org/packages/deltaCaptureC
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/deltaCaptureC
Package Short Url	https://bioconductor.org/packages/deltaCaptureC/
Package Downloads Report	Download Stats