geneRxCluster

This package is for version 3.7 of Bioconductor; for the stable, up-to-date release version, see geneRxCluster.

gRx Differential Clustering


Bioconductor version: 3.7

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>

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

Installation

To install this package, start R (version "3.5") and enter:


if (!require("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")
Using geneRxCluster PDF R Script
Reference Manual PDF

Details

biocViews Clustering, Genetics, Sequencing, Software
Version 1.16.0
In Bioconductor since BioC 2.14 (R-3.1) (10 years)
License GPL (>= 2)
Depends GenomicRanges, IRanges
Imports
System Requirements
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Suggests RUnit, BiocGenerics
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Package Archives

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

Source Package geneRxCluster_1.16.0.tar.gz
Windows Binary geneRxCluster_1.16.0.zip (32- & 64-bit)
Mac OS X 10.11 (El Capitan) geneRxCluster_1.16.0.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
Old Source Packages for BioC 3.7 Source Archive