deltaCaptureC

This package is for version 3.15 of Bioconductor; for the stable, up-to-date release version, see deltaCaptureC.

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


Bioconductor version: 3.15

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 <michael.shapiro at crick.ac.uk>

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

Installation

To install this package, start R (version "4.2") and enter:


if (!require("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")
Delta Capture-C HTML R Script
Reference Manual PDF
LICENSE Text

Details

biocViews BiologicalQuestion, Software, StatisticalMethod
Version 1.10.0
In Bioconductor since BioC 3.10 (R-3.6) (4.5 years)
License MIT + file LICENSE
Depends R (>= 3.6)
Imports IRanges, GenomicRanges, SummarizedExperiment, ggplot2, DESeq2, tictoc
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Suggests knitr, rmarkdown
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Package Archives

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

Source Package deltaCaptureC_1.10.0.tar.gz
Windows Binary deltaCaptureC_1.10.0.zip
macOS Binary (x86_64) deltaCaptureC_1.10.0.tgz
Source Repository git clone https://git.bioconductor.org/packages/deltaCaptureC
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/deltaCaptureC
Bioc Package Browser https://code.bioconductor.org/browse/deltaCaptureC/
Package Short Url https://bioconductor.org/packages/deltaCaptureC/
Package Downloads Report Download Stats
Old Source Packages for BioC 3.15 Source Archive