Files in lima1/PureCN
Copy number calling and SNV classification using targeted short read sequencing
.Rbuildignore
.github/.gitignore
.github/ISSUE_TEMPLATE/issue-report.md
.github/workflows/check-bioc.yml
DESCRIPTION
Dockerfile
LICENSE
NAMESPACE
NEWS
R/PureCN-internal.R
R/adjustLogRatio.R
R/annotateTargets.R
R/bootstrapResults.R
R/calculateBamCoverageByInterval.R
R/calculateLogRatio.R
R/calculateMappingBiasVcf.R
R/callAlterations.R
R/callAmplificationsInLowPurity.R
R/callCIN.R
R/callLOH.R
R/callMutationBurden.R
R/correctCoverageBias.R
R/createCurationFile.R
R/createNormalDatabase.R
R/filterIntervals.R
R/filterVcf.R
R/filterVcfMuTect.R
R/filterVcfMuTect2.R
R/findFocal.R
R/getSex.R
R/plotAbs.R
R/poolCoverage.R
R/powerDetectSomatic.R
R/predictSomatic.R
R/preprocessIntervals.R
R/processMultipleSamples.R
R/readAllelicCountsFile.R
R/readCoverageFile.R
R/readCurationFile.R
R/readIntervalFile.R
R/readLogRatioFile.R
R/readSegmentationFile.R
R/runAbsoluteCN.R
R/segmentationCBS.R
R/segmentationGATK4.R
R/segmentationHclust.R
R/segmentationPSCBS.R
R/setMappingBiasVcf.R
R/setPriorVcf.R
README.md
data/centromeres.rda
data/purecn.DNAcopy.bdry.rda
data/purecn.example.output.rda
inst/CITATION
inst/extdata/BenchmarkTumorOnly.R
inst/extdata/Coverage.R
inst/extdata/Dx.R
inst/extdata/FilterCallableLoci.R
inst/extdata/IntervalFile.R
inst/extdata/NormalDB.R
inst/extdata/PureCN.R
inst/extdata/buggy_cnvkit.seg.gz
inst/extdata/dist/calculateSbdry.R
inst/extdata/dist/downloadCentromeres.R
inst/extdata/ex1.bam
inst/extdata/ex1.bam.bai
inst/extdata/ex1_gcgene.txt
inst/extdata/ex1_intervals.txt
inst/extdata/ex1_intervals_headered.txt
inst/extdata/ex2_intervals.bed
inst/extdata/ex2_intervals.txt
inst/extdata/ex2_mappability.bed
inst/extdata/ex2_mappability.bigWig
inst/extdata/ex2_reference.fa
inst/extdata/ex2_reference.fa.fai
inst/extdata/ex2_reptiming.bed
inst/extdata/ex3_intervals.bed
inst/extdata/ex3_mappability.bed
inst/extdata/ex3_reference.fa
inst/extdata/ex3_reference.fa.fai
inst/extdata/example.vcf.gz
inst/extdata/example_allelic_counts.tsv
inst/extdata/example_callable.bed.gz
inst/extdata/example_cosmic.vcf.gz
inst/extdata/example_cosmic.vcf.gz.tbi
inst/extdata/example_gatk4_denoised_cr.tsv.gz
inst/extdata/example_gatk4_modelfinal.seg.gz
inst/extdata/example_intervals.txt
inst/extdata/example_intervals_tiny.txt
inst/extdata/example_intervals_tiny_ot.txt.gz
inst/extdata/example_logratio.txt.gz
inst/extdata/example_mutect2.vcf.gz
inst/extdata/example_mutect2.vcf.gz.tbi
inst/extdata/example_normal.list
inst/extdata/example_normal.txt.gz
inst/extdata/example_normal2.txt.gz
inst/extdata/example_normal3.cnn
inst/extdata/example_normal4.cnr
inst/extdata/example_normal5.hdf5
inst/extdata/example_normal_tiny.txt
inst/extdata/example_seg.txt
inst/extdata/example_single.vcf.gz
inst/extdata/example_single.vcf.gz.tbi
inst/extdata/example_tumor.txt.gz
inst/extdata/example_tumor2.txt.gz
inst/extdata/example_tumor_tiny.txt
inst/extdata/example_vcf.vcf.gz
inst/extdata/example_vcf.vcf.gz.tbi
inst/extdata/gatk4_m2_test_pon_db.tgz
inst/extdata/gatk4_pon_db.tgz
inst/extdata/issue109.vcf.gz
inst/extdata/issue184.vcf.gz
inst/extdata/issue184_2.vcf.gz
inst/extdata/issue184_2_mb.rds
inst/extdata/issue192_tumor.cnr
inst/extdata/issue192_tumor.seg
inst/extdata/issue62.vcf.gz
inst/extdata/issue62.vcf.gz.tbi
inst/extdata/normalpanel.vcf.gz
inst/extdata/normalpanel.vcf.gz.tbi
inst/extdata/test_coverage_overlapping_intervals.txt
man/PureCN-defunct.Rd
man/PureCN-deprecated.Rd
man/adjustLogRatio.Rd
man/annotateTargets.Rd
man/bootstrapResults.Rd
man/calculateBamCoverageByInterval.Rd
man/calculateLogRatio.Rd
man/calculateMappingBiasGatk4.Rd
man/calculateMappingBiasVcf.Rd
man/calculatePowerDetectSomatic.Rd
man/calculateTangentNormal.Rd
man/callAlterations.Rd
man/callAlterationsFromSegmentation.Rd
man/callAmplificationsInLowPurity.Rd
man/callCIN.Rd
man/callLOH.Rd
man/callMutationBurden.Rd
man/centromeres.Rd
man/correctCoverageBias.Rd
man/createCurationFile.Rd
man/createNormalDatabase.Rd
man/filterIntervals.Rd
man/filterVcfBasic.Rd
man/filterVcfMuTect.Rd
man/filterVcfMuTect2.Rd
man/findFocal.Rd
man/findHighQualitySNPs.Rd
man/getSexFromCoverage.Rd
man/getSexFromVcf.Rd
man/plotAbs.Rd
man/poolCoverage.Rd
man/predictSomatic.Rd
man/preprocessIntervals.Rd
man/processMultipleSamples.Rd
man/purecn.DNAcopy.bdry.Rd
man/purecn.example.output.Rd
man/readAllelicCountsFile.Rd
man/readCoverageFile.Rd
man/readCurationFile.Rd
man/readIntervalFile.Rd
man/readLogRatioFile.Rd
man/readSegmentationFile.Rd
man/runAbsoluteCN.Rd
man/segmentationCBS.Rd
man/segmentationGATK4.Rd
man/segmentationHclust.Rd
man/segmentationPSCBS.Rd
man/setMappingBiasVcf.Rd
man/setPriorVcf.Rd
tests/testthat.R
tests/testthat/test_adjustLogRatio.R
tests/testthat/test_annotateTargets.R
tests/testthat/test_bootstrapResults.R
tests/testthat/test_calculateBamCoverageByInterval.R
tests/testthat/test_calculateLogRatio.R
tests/testthat/test_calculatePowerDetectSomatic.R
tests/testthat/test_callAlterations.R
tests/testthat/test_callAlterationsFromSegmentation.R
tests/testthat/test_callAmplificationsInLowPurity.R
tests/testthat/test_callCIN.R
tests/testthat/test_callLOH.R
tests/testthat/test_callMutationBurden.R
tests/testthat/test_correctCoverageBias.R
tests/testthat/test_createCurationFile.R
tests/testthat/test_createNormalDatabase.R
tests/testthat/test_filterVcf.R
tests/testthat/test_findFocal.R
tests/testthat/test_getSexFromCoverage.R
tests/testthat/test_getSexFromVcf.R
tests/testthat/test_plotAbs.R
tests/testthat/test_poolCoverage.R
tests/testthat/test_predictSomatic.R
tests/testthat/test_preprocessIntervals.R
tests/testthat/test_readAllelicCountsFile.R
tests/testthat/test_readCoverageFile.R
tests/testthat/test_readLogRatioFile.R
tests/testthat/test_readSegmentationFile.R
tests/testthat/test_runAbsoluteCN.R
tests/testthat/test_segmentation.R
tests/testthat/test_setMappingBiasVcf.R
tests/testthat/test_setPriorVcf.R
vignettes/PureCN.Rnw
vignettes/PureCN.bib
vignettes/Quick.Rmd
