Package: PureCN 2.13.0

Markus Riester

PureCN: Copy number calling and SNV classification using targeted short read sequencing

This package estimates tumor purity, copy number, and loss of heterozygosity (LOH), and classifies single nucleotide variants (SNVs) by somatic status and clonality. PureCN is designed for targeted short read sequencing data, integrates well with standard somatic variant detection and copy number pipelines, and has support for tumor samples without matching normal samples.

Authors:Markus Riester [aut, cre], Angad P. Singh [aut]

PureCN_2.13.0.tar.gz
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PureCN.pdf |PureCN.html✨
PureCN/json (API)
NEWS

# Install 'PureCN' in R:
install.packages('PureCN', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org'))

Peer review:

Bug tracker:https://github.com/lima1/purecn/issues

Datasets:

On BioConductor:PureCN-2.13.0(bioc 3.21)PureCN-2.12.0(bioc 3.20)

copynumbervariationsoftwaresequencingvariantannotationvariantdetectioncoverageimmunooncologybioconductor-packagecell-free-dnacopy-numberlohtumor-heterogeneitytumor-mutational-burdentumor-purity

9.71 score 128 stars 52 scripts 406 downloads 11 mentions 43 exports 98 dependencies

Last updated 2 months agofrom:cb8d0f6c89. Checks:OK: 3 NOTE: 4. Indexed: yes.

TargetResultDate
Doc / VignettesOKNov 30 2024
R-4.5-winOKNov 30 2024
R-4.5-linuxOKNov 30 2024
R-4.4-winNOTENov 30 2024
R-4.4-macNOTENov 30 2024
R-4.3-winNOTENov 30 2024
R-4.3-macNOTENov 30 2024

Exports:adjustLogRatioannotateTargetsbootstrapResultscalculateBamCoverageByIntervalcalculateLogRatiocalculateMappingBiasGatk4calculateMappingBiasVcfcalculatePowerDetectSomaticcalculateTangentNormalcallAlterationscallAlterationsFromSegmentationcallAmplificationsInLowPuritycallCINcallLOHcallMutationBurdencorrectCoverageBiascreateCurationFilecreateNormalDatabasefilterIntervalsfilterVcfBasicfilterVcfMuTectfilterVcfMuTect2findFocalgetSexFromCoveragegetSexFromVcfplotAbspoolCoveragepredictSomaticpreprocessIntervalsprocessMultipleSamplesreadAllelicCountsFilereadCoverageFilereadCurationFilereadIntervalFilereadLogRatioFilereadSegmentationFilerunAbsoluteCNsegmentationCBSsegmentationGATK4segmentationHclustsegmentationPSCBSsetMappingBiasVcfsetPriorVcf

Dependencies:abindAnnotationDbiaskpassBHBiobaseBiocGenericsBiocIOBiocParallelBiostringsbitbit64bitopsblobBSgenomecachemclicodetoolscolorspacecpp11crayoncurldata.tableDBIDelayedArrayDNAcopyfansifarverfastmapformatRfutile.loggerfutile.optionsgenericsGenomeInfoDbGenomeInfoDbDataGenomicAlignmentsGenomicFeaturesGenomicRangesggplot2gluegridExtragtablehttrIRangesisobandjsonliteKEGGRESTlabelinglambda.rlatticelifecyclemagrittrMASSMatrixMatrixGenericsmatrixStatsmclustmemoisemgcvmimemunsellnlmeopensslpillarpkgconfigplogrpngR6RColorBrewerRCurlrestfulrrhdf5rhdf5filtersRhdf5libRhtslibrjsonrlangRsamtoolsRSQLitertracklayerS4ArraysS4VectorsscalessnowSparseArraySummarizedExperimentsystibbleUCSC.utilsutf8VariantAnnotationvctrsVGAMviridisLitewithrXMLXVectoryamlzlibbioc

PureCN best practices

Markus Riester

Rendered fromQuick.Rmdusingknitr::rmarkdownon Nov 30 2024.

Last update: 2023-12-11
Started: 2019-08-31

Overview of the PureCN R package

Rendered fromPureCN.Rnwusingknitr::knitron Nov 30 2024.

Last update: 2023-12-11
Started: 2016-04-14

Readme and manuals

Help Manual

Help pageTopics
Adjust tumor vs. normal coverage log ratio for tumor purity and ploidyadjustLogRatio
Annotate targets with gene symbolsannotateTargets
Bootstrapping variant fitsbootstrapResults
Function to calculate coverage from BAM filecalculateBamCoverageByInterval
Calculate coverage log-ratio of tumor vs. normalcalculateLogRatio
Calculate Mapping Bias from GATK4 GenomicsDBcalculateMappingBiasGatk4
Calculate Mapping BiascalculateMappingBiasVcf
Power calculation for detecting somatic mutationscalculatePowerDetectSomatic
Calculate tangent normalcalculateTangentNormal
Calling of amplifications and deletionscallAlterations
Calling of amplifications and deletions from segmentationscallAlterationsFromSegmentation
Calling of amplifications in low purity samplescallAmplificationsInLowPurity
Call Chromosomal InstabilitycallCIN
Get regions of LOHcallLOH
Call mutation burdencallMutationBurden
A list of data.frames containing centromere positions.centromeres
Correct for library-specific coverage biasescorrectCoverageBias
Create file to curate PureCN resultscreateCurationFile
Create database of normal samplescreateNormalDatabase
Remove low quality intervalsfilterIntervals
Basic VCF filter functionfilterVcfBasic
Filter VCF MuTectfilterVcfMuTect
Filter VCF MuTect2filterVcfMuTect2
Find focal amplificationsfindFocal
Get sample sex from coveragegetSexFromCoverage
Get sample sex from a VCF filegetSexFromVcf
Plots for analyzing PureCN solutionsplotAbs
Pool coverage from multiple samplespoolCoverage
Predict germline vs. somatic statuspredictSomatic
Preprocess intervalspreprocessIntervals
Multi sample normalization and segmentationprocessMultipleSamples
Defunct functions in package 'PureCN'PureCN-defunct
Deprecated functions in package 'PureCN'PureCN-deprecated
DNAcopy boundary datapurecn.DNAcopy.bdry
Example outputpurecn.example.output
Read allelic counts filereadAllelicCountsFile
Read coverage filereadCoverageFile
Read curation filereadCurationFile
Read interval filereadIntervalFile
Read file containing interval-level log2 tumor/normal ratiosreadLogRatioFile
Read file containing segmentationsreadSegmentationFile
Run PureCN implementation of ABSOLUTErunAbsoluteCN
CBS segmentationsegmentationCBS
GATK4 ModelSegments segmentation functionsegmentationGATK4
Minimal segmentation functionsegmentationHclust
PSCBS segmentationsegmentationPSCBS
Set Mapping Bias VCFsetMappingBiasVcf
Set Somatic Prior VCFsetPriorVcf