Files in benilton/crlmm-release
Genotype Calling (CRLMM) and Copy Number Analysis tool for Affymetrix SNP 5.0 and 6.0 and Illumina arrays.
.Rinstignore
.gitignore
CHANGES
DESCRIPTION
NAMESPACE
R/AllClasses.R
R/AllGenerics.R
R/cnrma-functions.R
R/cnset-accessors.R
R/crlmm-functions.R
R/crlmm-illumina.R
R/crlmmGT2.R
R/krlmm.R
R/methods-AssayData.R
R/methods-CNSet.R
R/methods-CNSetLM.R
R/methods-PredictionRegion.R
R/methods-SnpSuperSet.R
R/methods-eSet.R
R/snprma-functions.R
R/test_crlmm_package.R
R/utils.R
R/zzz.R
TODO
data/cnSetExample.rda
data/cnSetExample2.rda
inst/CITATION
inst/NEWS.Rd
inst/scripts/.gitignore
inst/scripts/AffyGW.Rnw
inst/scripts/AffyGW.pdf
inst/scripts/IlluminaPreprocessCN.Rnw
inst/scripts/IlluminaPreprocessCN.pdf
inst/scripts/Infrastructure.Rnw
inst/scripts/Infrastructure.pdf
inst/scripts/Makefile
inst/scripts/copynumber.Rnw
inst/scripts/crlmmDownstream.pdf
inst/scripts/crlmmIllumina.Rnw
inst/scripts/crlmmIllumina.pdf
inst/scripts/gtypeDownstream.Rnw
inst/scripts/gtypeDownstream.pdf
inst/scripts/refs.bib
inst/scripts/sync
inst/unitTests/Makefile
inst/unitTests/test_crlmm.R
inst/unitTests/test_dataExamples.R
inst/unitTests/test_ff.R
man/.DS_Store
man/ABpanel.Rd
man/AssayData-methods.Rd
man/CNSet-methods.Rd
man/ListClassConstructors.Rd
man/PredictionRegion-class.Rd
man/batchStatisticAccessors.Rd
man/calculateRBaf.Rd
man/celfile-utils.Rd
man/cnSetExample.Rd
man/cnrmaAffy.Rd
man/constructAffyCNSet.Rd
man/constructInf.Rd
man/copynumberAccessors.Rd
man/crlmm-package.Rd
man/crlmm.Rd
man/crlmmCopynumber.Rd
man/crlmmIllumina.Rd
man/crlmmIlluminaV2.Rd
man/genotype.Illumina.Rd
man/genotype.Rd
man/genotypeAffy.Rd
man/genotypeInf.Rd
man/genotypes.Rd
man/posteriorProbability.Rd
man/predictionRegion.Rd
man/preprocessInf.Rd
man/readGenCallOutput.Rd
man/readIdatFiles.Rd
man/snprma.Rd
man/snprmaAffy.Rd
man/validCdfNames.Rd
man/xyplot.Rd
src/crlmm.h
src/gtypeCaller.c
src/init.c
src/trimmed.c
src/utils.c
src/utils.h
tests/crlmm_unit_tests.R
tests/doRUnit.R
vignettes/AffyGW.Rnw
vignettes/CopyNumberOverview.Rnw
vignettes/IlluminaPreprocessCN.Rnw
vignettes/Infrastructure.Rnw
vignettes/Makefile
vignettes/genotyping.Rnw
vignettes/gtypeDownstream.Rnw
