geneRxCluster

gRx Differential Clustering

Bioconductor version: Development (3.0)

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>

To install this package, start R and enter:

source("http://bioconductor.org/biocLite.R")
biocLite("geneRxCluster")

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

Documentation

PDF R Script Using geneRxCluster
PDF   Reference Manual

Details

biocViews Clustering, Genetics, Sequencing, Software
Version 1.1.0
In Bioconductor since BioC 2.14 (R-3.1)
License GPL (>= 2)
Depends GenomicRanges, IRanges
Imports
Suggests RUnit, BiocGenerics
System Requirements
URL
Depends On Me
Imports Me
Suggests Me

Package Downloads

Package Source geneRxCluster_1.1.0.tar.gz
Windows Binary geneRxCluster_1.1.0.zip (32- & 64-bit)
Mac OS X 10.6 (Snow Leopard) geneRxCluster_1.1.0.tgz
Mac OS X 10.9 (Mavericks) geneRxCluster_1.1.0.tgz
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