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>
citation("geneRxCluster")):
Installation
To install this package, start R (version "3.6") 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 | R Script | |
| Reference Manual |
Details
| biocViews | Clustering, Genetics, Sequencing, Software |
| Version | 1.20.0 |
| In Bioconductor since | BioC 2.14 (R-3.1) (10 years) |
| License | GPL (>= 2) |
| Depends | GenomicRanges, IRanges |
| Imports | |
| System Requirements | |
| URL |
See More
| Suggests | RUnit, BiocGenerics |
| Linking To | |
| Enhances | |
| Depends On Me | |
| Imports Me | |
| Suggests Me | |
| Links To Me | |
| Build Report | 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 [email protected]:packages/geneRxCluster |
| Bioc Package Browser | https://code.bioconductor.org/browse/geneRxCluster/ |
| Package Short Url | https://bioconductor.org/packages/geneRxCluster/ |
| Package Downloads Report | Download Stats |
| Old Source Packages for BioC 3.9 | Source Archive |