Package: PlasmaMutationDetector2 1.1.11

PlasmaMutationDetector2: Tumor Mutation Detection in Plasma using Barcoding

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 using barcoding. Mutations are assessed by comparing the minor-allele frequency at each position to the measured PER in control samples. This package has been used for Kjersti Tjensvoll, Morten Lapin, Bjørnar Gilje, Herish Garresori, Satu Oltedal, Rakel Brendsdal Forthun, Anders Molven, Yves Rozenholc and Oddmund N\o{o}rdgaard (2022) <https://www.nature.com/articles/s41598-022-09698-5>.

Authors:Yves Rozenholc [cre, aut] Oddmund Nordgård [con, aut] Nicolas Pécuchet [con] Pierre-Laurent Puig [con]

PlasmaMutationDetector2_1.1.11.tar.gz
PlasmaMutationDetector2_1.1.11.zip(r-4.5)PlasmaMutationDetector2_1.1.11.zip(r-4.4)PlasmaMutationDetector2_1.1.11.zip(r-4.3)
PlasmaMutationDetector2_1.1.11.tgz(r-4.4-any)PlasmaMutationDetector2_1.1.11.tgz(r-4.3-any)
PlasmaMutationDetector2_1.1.11.tar.gz(r-4.5-noble)PlasmaMutationDetector2_1.1.11.tar.gz(r-4.4-noble)
PlasmaMutationDetector2_1.1.11.tgz(r-4.4-emscripten)PlasmaMutationDetector2_1.1.11.tgz(r-4.3-emscripten)
PlasmaMutationDetector2.pdf |PlasmaMutationDetector2.html✨
PlasmaMutationDetector2/json (API)

# Install 'PlasmaMutationDetector2' in R:
install.packages('PlasmaMutationDetector2', repos = c('https://yrozen-biostm.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'.

On CRAN:

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

1.00 score 120 downloads 5 exports 92 dependencies

Last updated 3 years agofrom:32535767c4. Checks:OK: 1 WARNING: 1 NOTE: 5. Indexed: yes.

TargetResultDate
Doc / VignettesOKNov 15 2024
R-4.5-winNOTENov 15 2024
R-4.5-linuxWARNINGNov 15 2024
R-4.4-winNOTENov 15 2024
R-4.4-macNOTENov 15 2024
R-4.3-winNOTENov 15 2024
R-4.3-macNOTEOct 16 2024

Exports:BuildCtrlErrorRateDetectPlasmaMutationLoadBackgroundErrorRateMAF_from_BAMPrepareLibrary

Dependencies:abindAnnotationDbiaskpassBHBiobaseBiocGenericsBiocIOBiocParallelBiostringsbitbit64bitopsblobBSgenomecachemclicodetoolscolorspacecpp11crayoncurlDBIDelayedArrayDEoptimRfansifarverfastmapformatRfutile.loggerfutile.optionsgenericsGenomeInfoDbGenomeInfoDbDataGenomicAlignmentsGenomicFeaturesGenomicRangesggplot2gluegtablehttrIRangesisobandjsonliteKEGGRESTlabelinglambda.rlatticelifecyclemagrittrMASSMatrixMatrixGenericsmatrixStatsmemoisemgcvmimemunsellnlmeopensslpillarpkgconfigplogrpngR6RColorBrewerRCurlrestfulrRhtslibrjsonrlangrobustbaseRsamtoolsRSQLitertracklayerS4ArraysS4VectorsscalessnowSparseArraySummarizedExperimentsystibbleUCSC.utilsutf8VariantAnnotationvctrsviridisLitewithrXMLXVectoryamlzlibbioc