Files in PureCN

Copy number calling and SNV classification using targeted short read sequencing

README.md

NEWS

NAMESPACE

DESCRIPTION

build/vignette.rds

data/centromeres.rda

data/purecn.DNAcopy.bdry.rda

data/purecn.example.output.rda

R/readSegmentationFile.R R/PureCN-internal.R R/poolCoverage.R R/filterVcfMuTect.R R/calculateIntervalWeights.R R/readCoverageFile.R R/bootstrapResults.R R/powerDetectSomatic.R R/processMultipleSamples.R R/segmentationHclust.R R/callMutationBurden.R R/filterIntervals.R R/correctCoverageBias.R R/setMappingBiasVcf.R R/calculateLogRatio.R R/runAbsoluteCN.R R/filterVcfMuTect2.R R/plotAbs.R R/segmentationPSCBS.R R/createNormalDatabase.R R/getSex.R R/readCurationFile.R R/findFocal.R R/callAmplificationsInLowPurity.R R/readLogRatioFile.R R/calculateBamCoverageByInterval.R R/preprocessIntervals.R R/predictSomatic.R R/filterVcf.R R/annotateTargets.R R/calculateMappingBiasVcf.R R/callLOH.R R/createCurationFile.R R/callAlterations.R R/setPriorVcf.R R/segmentationCBS.R R/callCIN.R vignettes/Quick.Rmd

vignettes/PureCN.Rnw

vignettes/PureCN.bib

man/callMutationBurden.Rd man/readCurationFile.Rd man/calculateTangentNormal.Rd man/PureCN-defunct.Rd man/calculatePowerDetectSomatic.Rd man/findFocal.Rd man/calculateMappingBiasGatk4.Rd man/segmentationPSCBS.Rd man/calculateLogRatio.Rd man/setMappingBiasVcf.Rd man/calculateBamCoverageByInterval.Rd man/createCurationFile.Rd man/purecn.example.output.Rd man/PureCN-deprecated.Rd man/plotAbs.Rd man/calculateIntervalWeights.Rd man/filterVcfMuTect.Rd man/getSexFromVcf.Rd man/callAmplificationsInLowPurity.Rd man/annotateTargets.Rd man/getSexFromCoverage.Rd man/createNormalDatabase.Rd man/readLogRatioFile.Rd man/bootstrapResults.Rd man/predictSomatic.Rd man/setPriorVcf.Rd man/segmentationCBS.Rd man/correctCoverageBias.Rd man/readCoverageFile.Rd man/callAlterationsFromSegmentation.Rd man/readSegmentationFile.Rd man/purecn.DNAcopy.bdry.Rd man/callAlterations.Rd man/segmentationHclust.Rd man/preprocessIntervals.Rd man/runAbsoluteCN.Rd man/poolCoverage.Rd man/processMultipleSamples.Rd man/callLOH.Rd man/calculateMappingBiasVcf.Rd man/filterVcfMuTect2.Rd man/callCIN.Rd man/filterIntervals.Rd man/filterVcfBasic.Rd man/centromeres.Rd tests/testthat.R tests/testthat/test_setPriorVcf.R tests/testthat/test_callMutationBurden.R tests/testthat/test_callCIN.R tests/testthat/test_readCoverageFile.R tests/testthat/test_plotAbs.R tests/testthat/test_callAlterationsFromSegmentation.R tests/testthat/test_correctCoverageBias.R tests/testthat/test_createCurationFile.R tests/testthat/test_readSegmentationFile.R tests/testthat/test_setMappingBiasVcf.R tests/testthat/test_getSexFromCoverage.R tests/testthat/test_predictSomatic.R tests/testthat/test_bootstrapResults.R tests/testthat/test_processMultipleSamples.R tests/testthat/test_callAmplificationsInLowPurity.R tests/testthat/test_runAbsoluteCN.R tests/testthat/test_createNormalDatabase.R tests/testthat/test_calculatePowerDetectSomatic.R tests/testthat/test_callLOH.R tests/testthat/test_preprocessIntervals.R tests/testthat/test_getSexFromVcf.R tests/testthat/test_poolCoverage.R tests/testthat/test_readLogRatioFile.R tests/testthat/test_calculateBamCoverageByInterval.R tests/testthat/test_callAlterations.R tests/testthat/test_segmentation.R tests/testthat/test_findFocal.R tests/testthat/test_filterVcf.R tests/testthat/test_annotateTargets.R

inst/CITATION

inst/doc/Quick.html

inst/doc/Quick.Rmd

inst/doc/PureCN.Rnw

inst/doc/PureCN.pdf inst/doc/Quick.R inst/doc/PureCN.R

inst/extdata/example_mutect2.vcf.gz

inst/extdata/example_normal.list

inst/extdata/gatk4_pon_db.tgz

inst/extdata/example_vcf.vcf.gz

inst/extdata/issue62.vcf.gz.tbi

inst/extdata/buggy_cnvkit.seg.gz

inst/extdata/example_intervals.txt

inst/extdata/FilterCallableLoci.R

inst/extdata/example_seg.txt

inst/extdata/ex1.bam

inst/extdata/example_tumor2.txt

inst/extdata/normalpanel.vcf.gz

inst/extdata/example_single.vcf.gz

inst/extdata/ex2_reptiming.bed

inst/extdata/ex2_mappability.bed

inst/extdata/example_cosmic.vcf.gz

inst/extdata/ex3_mappability.bed

inst/extdata/example_tumor_tiny.txt

inst/extdata/example_normal3.cnn

inst/extdata/ex2_intervals.bed

inst/extdata/example_tumor.txt

inst/extdata/issue109.vcf.gz

inst/extdata/ex2_intervals.txt

inst/extdata/BenchmarkTumorOnly.R

inst/extdata/example_normal.txt

inst/extdata/example_intervals_tiny.txt

inst/extdata/ex2_reference.fa.fai

inst/extdata/ex1.bam.bai

inst/extdata/example_normal2.txt

inst/extdata/ex3_reference.fa

inst/extdata/Dx.R

inst/extdata/ex3_intervals.bed

inst/extdata/example_gatk4_modelfinal.seg.gz

inst/extdata/ex1_intervals.txt

inst/extdata/example_normal5.hdf5

inst/extdata/test_coverage_overlapping_intervals.txt

inst/extdata/example_mutect2.vcf.gz.tbi

inst/extdata/ex2_reference.fa

inst/extdata/example_gatk4_denoised_cr.tsv.gz

inst/extdata/ex2_mappability.bigWig

inst/extdata/ex1_gcgene.txt

inst/extdata/example_logratio.txt.gz

inst/extdata/NormalDB.R

inst/extdata/example_single.vcf.gz.tbi

inst/extdata/normalpanel.vcf.gz.tbi

inst/extdata/PureCN.R

inst/extdata/ex3_reference.fa.fai

inst/extdata/example_normal_tiny.txt

inst/extdata/example_cosmic.vcf.gz.tbi

inst/extdata/example_normal4.cnr

inst/extdata/IntervalFile.R

inst/extdata/example_vcf.vcf.gz.tbi

inst/extdata/example.vcf.gz

inst/extdata/Coverage.R

inst/extdata/example_callable.bed.gz

inst/extdata/issue62.vcf.gz

inst/extdata/dist/calculateSbdry.R inst/extdata/dist/downloadCentromeres.R

PureCN documentation built on Nov. 8, 2020, 5:37 p.m.