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deltaCaptureC

This is the development version of deltaCaptureC; for the stable release version, see deltaCaptureC.

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


Bioconductor version: Development (3.19)

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 "4.4") and enter:


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

# The following initializes usage of Bioc devel
BiocManager::install(version='devel')

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

Details

biocViews BiologicalQuestion, Software, StatisticalMethod
Version 1.17.1
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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Package Archives

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

Source Package deltaCaptureC_1.17.1.tar.gz
Windows Binary
macOS Binary (x86_64) deltaCaptureC_1.17.1.tgz
macOS Binary (arm64)
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