Package: doppelgangR 1.35.0

Levi Waldron

doppelgangR: Identify likely duplicate samples from genomic or meta-data

The main function is doppelgangR(), which takes as minimal input a list of ExpressionSet object, and searches all list pairs for duplicated samples. The search is based on the genomic data (exprs(eset)), phenotype/clinical data (pData(eset)), and "smoking guns" - supposedly unique identifiers found in pData(eset).

Authors:Levi Waldron [aut, cre], Markus Reister [aut, ctb], Marcel Ramos [ctb]

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NEWS

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

Peer review:

Bug tracker:https://github.com/lwaldron/doppelgangr/issues

On BioConductor:doppelgangR-1.35.0(bioc 3.21)doppelgangR-1.34.0(bioc 3.20)

immunooncologyrnaseqmicroarraygeneexpressionqualitycontrolbioconductor-package

6.67 score 5 stars 31 scripts 412 downloads 3 mentions 19 exports 72 dependencies

Last updated 2 months agofrom:0cd0783571. Checks:OK: 1 NOTE: 6. Indexed: yes.

TargetResultDate
Doc / VignettesOKNov 29 2024
R-4.5-winNOTENov 29 2024
R-4.5-linuxNOTENov 29 2024
R-4.4-winNOTENov 29 2024
R-4.4-macNOTENov 29 2024
R-4.3-winNOTENov 29 2024
R-4.3-macNOTENov 29 2024

Exports:colFindercorFinderdoppelgangRdstmst.mleoutlierFinderphenoDistphenoFinderplotprintpstqstrstshowsmokingGunFinderst.mlesummaryvectorHammingDistvectorWeightedDist

Dependencies:abindannotateAnnotationDbiaskpassBHBiobaseBiocGenericsBiocParallelBiostringsbitbit64blobcachemclicodetoolscpp11crayoncurlDBIDelayedArraydigestedgeRfastmapformatRfutile.loggerfutile.optionsgenefiltergenericsGenomeInfoDbGenomeInfoDbDataGenomicRangesgluehttrimputeIRangesjsonliteKEGGRESTlambda.rlatticelifecyclelimmalocfitMatrixMatrixGenericsmatrixStatsmemoisemgcvmimemnormtnlmeopensslpkgconfigplogrpngR6rlangRSQLiteS4ArraysS4VectorssnowSparseArraystatmodSummarizedExperimentsurvivalsvasysUCSC.utilsvctrsXMLxtableXVectorzlibbioc

doppelgangR

Levi Waldron

Rendered fromdoppelgangR.Rmdusingknitr::rmarkdownon Nov 29 2024.

Last update: 2016-03-17
Started: 2016-03-17