deltaCaptureC

DOI: 10.18129/B9.bioc.deltaCaptureC    

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

Bioconductor version: Release (3.10)

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>

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

Installation

To install this package, start R (version "3.6") 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 1.0.0
In Bioconductor since BioC 3.10 (R-3.6) (< 6 months)
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_1.0.0.tar.gz
Windows Binary deltaCaptureC_1.0.0.zip
Mac OS X 10.11 (El Capitan) deltaCaptureC_1.0.0.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

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