Package: PlasmaMutationDetector 1.7.2

Yves Rozenholc

PlasmaMutationDetector: Tumor Mutation Detection in Plasma

Aims at detecting single nucleotide variation (SNV) and insertion/deletion (INDEL) in circulating tumor DNA (ctDNA), used as a surrogate marker for tumor, at each base position of an Next Generation Sequencing (NGS) analysis. Mutations are assessed by comparing the minor-allele frequency at each position to the measured PER in control samples.

Authors:Yves Rozenholc, Nicolas Pécuchet, Pierre Laurent-Puig

PlasmaMutationDetector_1.7.2.tar.gz
PlasmaMutationDetector_1.7.2.tar.gz(r-4.5-noble)PlasmaMutationDetector_1.7.2.tar.gz(r-4.4-noble)
PlasmaMutationDetector_1.7.2.tgz(r-4.4-emscripten)PlasmaMutationDetector_1.7.2.tgz(r-4.3-emscripten)
PlasmaMutationDetector.pdf |PlasmaMutationDetector.html✨
PlasmaMutationDetector/json (API)

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

Peer review:

Datasets:
  • background_error_rate - The package provide the SNV and INDEL PERs computed for the Ion AmpliSeq™ Colon and Lung Cancer Panel v2 from 29 controls in a table available in the data file 'background_error_rate.txt'.
  • hotspot - The package provide a list of known hotspot positions located on the amplicons of the Ion AmpliSeq™ Colon and Lung Cancer Panel v2 as a txt file 'hotspot.txt' which contains a vector/variable -named chrpos (first row)- of chars, of the form chrN:XXXXXXXXX defining genomic positions.
  • pos_ind - The package provide the positions and ranges computed for the Ion AmpliSeq™ Colon and Lung Cancer Panel v2 as a Rdata file 'positions_ranges.rda'.
  • pos_ranges - The package provide the positions and ranges computed for the Ion AmpliSeq™ Colon and Lung Cancer Panel v2 as a Rdata file 'positions_ranges.rda'.
  • pos_snp - The package provide the positions and ranges computed for the Ion AmpliSeq™ Colon and Lung Cancer Panel v2 as a Rdata file 'positions_ranges.rda'.

This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.

1.30 score 197 downloads 2 mentions 4 exports 92 dependencies

Last updated 6 years agofrom:9a5b641f80. Checks:OK: 1 WARNING: 1. Indexed: yes.

TargetResultDate
Doc / VignettesOKNov 15 2024
R-4.5-linuxWARNINGNov 15 2024

Exports:BuildCtrlErrorRateDetectPlasmaMutationMAF_from_BAMPrepareLibrary

Dependencies:abindAnnotationDbiaskpassBHBiobaseBiocGenericsBiocIOBiocParallelBiostringsbitbit64bitopsblobBSgenomecachemclicodetoolscolorspacecpp11crayoncurlDBIDelayedArrayDEoptimRfansifarverfastmapformatRfutile.loggerfutile.optionsgenericsGenomeInfoDbGenomeInfoDbDataGenomicAlignmentsGenomicFeaturesGenomicRangesggplot2gluegtablehttrIRangesisobandjsonliteKEGGRESTlabelinglambda.rlatticelifecyclemagrittrMASSMatrixMatrixGenericsmatrixStatsmemoisemgcvmimemunsellnlmeopensslpillarpkgconfigplogrpngR6RColorBrewerRCurlrestfulrRhtslibrjsonrlangrobustbaseRsamtoolsRSQLitertracklayerS4ArraysS4VectorsscalessnowSparseArraySummarizedExperimentsystibbleUCSC.utilsutf8VariantAnnotationvctrsviridisLitewithrXMLXVectoryamlzlibbioc