Package: RAIDS 1.3.0
RAIDS: Accurate Inference of Genetic Ancestry from Cancer Sequences
This package implements specialized algorithms that enable genetic ancestry inference from various cancer sequences sources (RNA, Exome and Whole-Genome sequences). This package also implements a simulation algorithm that generates synthetic cancer-derived data. This code and analysis pipeline was designed and developed for the following publication: Belleau, P et al. Genetic Ancestry Inference from Cancer-Derived Molecular Data across Genomic and Transcriptomic Platforms. Cancer Res 1 January 2023; 83 (1): 49–58.
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RAIDS.pdf |RAIDS.html✨
RAIDS/json (API)
NEWS
# Install 'RAIDS' in R: |
install.packages('RAIDS', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org')) |
Bug tracker:https://github.com/krasnitzlab/raids/issues
- demoKnownSuperPop1KG - The known super population ancestry of the demo 1KG reference profiles.
- demoPCA1KG - The PCA results of the demo 1KG reference dataset for demonstration purpose. Beware that the PCA has been run on a very small subset of the 1KG reference dataset and should not be used to call ancestry inference on a real profile.
- demoPCASyntheticProfiles - The PCA result of demo synthetic profiles projected on the demo subset 1KG reference PCA.
- demoPedigreeEx1 - The pedigree information about a demo profile called 'ex1'.
- matKNNSynthetic - A small 'data.frame' containing the inferred ancestry on the synthetic profiles.
- pedSynthetic - A small 'data.frame' containing the information related to synthetic profiles. The ancestry of the profiles used to generate the synthetic profiles must be present.
- snpPositionDemo - A small 'data.frame' containing the SNV information.
On BioConductor:RAIDS-1.3.0(bioc 3.20)RAIDS-1.2.0(bioc 3.19)
Last updated 2 months agofrom:8c31b43b86
Exports:add1KG2SampleGDSaddGeneBlockGDSRefAnnotaddRef2GDS1KGaddStudy1KgcomputeAncestryFromSyntheticFilecomputeKNNRefSamplecomputeKNNRefSyntheticcomputePCAMultiSyntheticcomputePCARefSamplecomputePoolSyntheticAncestryGrcomputeSyntheticROCcreateStudy2GDS1KGestimateAllelicFractiongenerateGDS1KGgenerateMapSnvSelgeneratePhase1KG2GDSgetRef1KGPopgroupChr1KGSNVidentifyRelativeprepPed1KGprepSyntheticpruningSamplerunExomeAncestryrunRNAAncestryselect1KGPopsnvListVCFsplitSelectByPopsyntheticGeno
Dependencies:abindAnnotationDbiAnnotationFilteraskpassbackportsBHBiobaseBiocGenericsBiocIOBiocParallelBiostringsbitbit64bitopsblobbootbroomBSgenomecachemclassclicliprcodetoolscpp11crayoncurldata.tableDBIDelayedArrayDNAcopydplyrensembldbfansifastmapforcatsforeachformatRformula.toolsfutile.loggerfutile.optionsgdsfmtgenericsGENESISGenomeInfoDbGenomeInfoDbDataGenomicAlignmentsGenomicFeaturesGenomicRangesglmnetglueGWASExactHWGWASToolshavenhmshttrigraphIRangesiteratorsjomojsonliteKEGGRESTlambda.rlatticelazyevallifecyclelme4lmtestlogistfmagrittrMASSMatrixMatrixGenericsMatrixModelsmatrixStatsmemoisemgcvmicemimeminqamitmlnlmenloptrnnetnumDerivopenssloperator.toolsordinalpanpillarpkgconfigplogrplyrpngprettyunitspROCprogressProtGenericspurrrquantregquantsmoothR6RcppRcppEigenRCurlreadrreshape2restfulrRhtslibrjsonrlangrpartRsamtoolsRSQLitertracklayerS4ArraysS4VectorssandwichSeqArraySeqVarToolsshapesnowSNPRelateSparseArraySparseMstringistringrSummarizedExperimentsurvivalsystibbletidyrtidyselecttzdbucminfUCSC.utilsutf8VariantAnnotationvctrsvroomwithrXMLXVectoryamlzlibbioczoo
Accurate Inference of Genetic Ancestry from Cancer-derived Sequences
Rendered fromRAIDS.Rmd
usingknitr::rmarkdown
on Jun 30 2024.Last update: 2023-10-12
Started: 2023-03-30
Population reference dataset GDS files
Rendered fromCreate_Reference_GDS_File.Rmd
usingknitr::rmarkdown
on Jun 30 2024.Last update: 2023-09-29
Started: 2023-08-14