geneRxCluster: gRx Differential Clustering

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.

AuthorCharles Berry
Date of publicationNone
MaintainerCharles Berry <ccberry@ucsd.edu>
LicenseGPL (>= 2)
Version1.10.0

View on Bioconductor

Files

geneRxCluster/DESCRIPTION
geneRxCluster/NAMESPACE
geneRxCluster/R
geneRxCluster/R/Rutils.R geneRxCluster/R/dot-gRxCluster.R geneRxCluster/R/gRxCluster.R geneRxCluster/R/gRxPlot.R geneRxCluster/R/gRxPlotClumps.R geneRxCluster/R/gRxSummary.R geneRxCluster/R/geneRxCluster-package.R geneRxCluster/R/grx_clust_Call.R
geneRxCluster/build
geneRxCluster/build/vignette.rds
geneRxCluster/inst
geneRxCluster/inst/CITATION
geneRxCluster/inst/doc
geneRxCluster/inst/doc/tutorial.R
geneRxCluster/inst/doc/tutorial.Rnw
geneRxCluster/inst/doc/tutorial.pdf
geneRxCluster/inst/unitTests
geneRxCluster/inst/unitTests/Makefile
geneRxCluster/inst/unitTests/runit.1.R
geneRxCluster/man
geneRxCluster/man/critVal.alpha.Rd geneRxCluster/man/critVal.power.Rd geneRxCluster/man/critVal.target.Rd geneRxCluster/man/gRxCluster-object.Rd geneRxCluster/man/gRxCluster.Rd geneRxCluster/man/gRxPlot.Rd geneRxCluster/man/gRxPlotClumps.Rd geneRxCluster/man/gRxSummary.Rd geneRxCluster/man/geneRxCluster.Rd geneRxCluster/man/noprune.Rd geneRxCluster/man/plot.cutpoints.Rd geneRxCluster/man/prune.loglik.Rd
geneRxCluster/src
geneRxCluster/src/cluster.c
geneRxCluster/tests
geneRxCluster/tests/doRunit.R
geneRxCluster/vignettes
geneRxCluster/vignettes/tutorial.Rnw

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