Files in akdess/CaSpER
Identify large-scale CNV events from single cell or bulk RNA-Seq data
.Rbuildignore
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.gitignore
CaSpER.Rproj
DESCRIPTION
NAMESPACE
R/HMMcopy.R
R/casper.R
R/loh.R
R/plots.R
R/preprocessing.R
R/segmentation.R
R/utility_functions.R
README.md
README.txt
data/hg19_cytoband.rda
data/hg38_cytoband.rda
data/maf.rda
data/meningioma_baf/MN-1137.snp
data/meningioma_baf/MN-1161.snp
data/meningioma_baf/MN-1171.snp
data/meningioma_baf/MN-1236.snp
data/meningioma_baf/MN-1237.snp
data/meningioma_baf/MN-5.snp
data/meningioma_baf/MN-60.snp
data/meningioma_baf/MN-60835.snp
data/scell_gbm.rda
data/tcga_gbm.rda
data/yale_meningioma.rda
demo/CaSpER_for_Mouse.R
demo/MM135_10X.R
demo/meningioma.R
demo/sCellGBM.R
demo/tcga_BRCA.R
demo/tcga_GBM.R
install_dependencies.R
install_dependencies.sh
man/AverageReference.Rd
man/CaSpER-package.Rd
man/CenterSmooth.Rd
man/ControlNormalize.Rd
man/CreateCasperObject.Rd
man/PerformMedianFilter.Rd
man/PerformMedianFilterByChr.Rd
man/PerformSegmentationWithHMM.Rd
man/ProcessData.Rd
man/assignStates.Rd
man/calcROC.Rd
man/calculateLOHShiftsForEachSegment.Rd
man/casper.Rd
man/extractEvents.Rd
man/extractLargeScaleEvents.Rd
man/extractMUAndCooccurence.Rd
man/extractSegmentSummary.Rd
man/gene.matrix.Rd
man/generateAnnotation.Rd
man/generateEnrichmentSummary.Rd
man/generateLargeScaleEvents.Rd
man/generateParam.Rd
man/getDiffExprGenes.Rd
man/goEnrichmentBP.Rd
man/hello.Rd
man/lohCallMedianFilter.Rd
man/lohCallMedianFilterByChr.Rd
man/mergeScalesAndGenerateFinalEventSummary.Rd
man/plotBAFAllSamples.Rd
man/plotBAFInSeperatePages.Rd
man/plotBAFOneSample.Rd
man/plotGEAllSamples.Rd
man/plotGEAndBAFOneSample.Rd
man/plotGEAndGT.Rd
man/plotHeatmap.Rd
man/plotLargeScaleEvent.Rd
man/plotLargeScaleEvent2.Rd
man/plotMUAndCooccurence.Rd
man/plotSCellCNVTree.Rd
man/plotSingleCellLargeScaleEventHeatmap.Rd
man/readBAFExtractOutput.Rd
man/runCaSpER.Rd
man/splitByOverlap.Rd
manual.pdf
src/CaSpER.dll
src/forward_backward.c
src/forward_backward.o
src/hmmcopy.h
src/register.c
src/register.o
src/viterbi.c
src/viterbi.o
vignettes/Introduction.R
vignettes/Introduction.Rmd
vignettes/Introduction.html
vignettes/Introduction.log
vignettes/LOHAllSamples.png
vignettes/MGH30network.png
vignettes/MN-5.png
vignettes/MN-5_GE_BAF.png
vignettes/MN-60.png
vignettes/RNASeqAndGT.png
vignettes/large.scale.events.png
vignettes/mgh31_ls.png
vignettes/rsconnect/documents/Introduction.Rmd/rpubs.com/rpubs/Document.dcf
vignettes/rsconnect/documents/Introduction.Rmd/rpubs.com/rpubs/Publish Document.dcf
vignettes/test.png
