geneRxCluster

DOI: 10.18129/B9.bioc.geneRxCluster    

This package is for version 3.9 of Bioconductor; for the stable, up-to-date release version, see geneRxCluster.

gRx Differential Clustering

Bioconductor version: 3.9

Detect Differential Clustering of Genomic Sites such as gene therapy integrations. The package provides some functions for exploring genomic insertion sites originating from two different sources. Possibly, the two sources are two different gene therapy vectors. Vectors are preferred that target sensitive regions less frequently, motivating the search for localized clusters of insertions and comparison of the clusters formed by integration of different vectors. Scan statistics allow the discovery of spatial differences in clustering and calculation of False Discovery Rates (FDRs) providing statistical methods for comparing retroviral vectors. A scan statistic for comparing two vectors using multiple window widths to detect clustering differentials and compute FDRs is implemented here.

Author: Charles Berry

Maintainer: Charles Berry <ccberry at ucsd.edu>

Installation

To install this package, start R (version "3.6") and enter:

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

BiocManager::install("geneRxCluster")

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("geneRxCluster")

 

PDF	R Script	Using geneRxCluster
PDF		Reference Manual

Details

biocViews	Clustering, Genetics, Sequencing, Software
Version	1.20.0
In Bioconductor since	BioC 2.14 (R-3.1) (5.5 years)
License	GPL (>= 2)
Depends	GenomicRanges, IRanges
Imports
LinkingTo
Suggests	RUnit, BiocGenerics
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	geneRxCluster_1.20.0.tar.gz
Windows Binary	geneRxCluster_1.20.0.zip
Mac OS X 10.11 (El Capitan)	geneRxCluster_1.20.0.tgz
Source Repository	git clone https://git.bioconductor.org/packages/geneRxCluster
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/geneRxCluster
Package Short Url	https://bioconductor.org/packages/geneRxCluster/
Package Downloads Report	Download Stats