Package: SingscoreAMLMutations 1.28.0

Dharmesh D. Bhuva

SingscoreAMLMutations: Using singscore to predict mutations in AML from transcriptomic signatures

This workflow package shows how transcriptomic signatures can be used to infer phenotypes. The workflow begins by showing how the TCGA AML transcriptomic data can be downloaded and processed using the TCGAbiolinks packages. It then shows how samples can be scored using the singscore package and signatures from the MSigDB. Finally, the predictive capacity of scores in the context of predicting a specific mutation in AML is shown.The workflow exhibits the interplay of Bioconductor packages to achieve a gene-set level analysis.

Authors:Dharmesh D. Bhuva [aut, cre], Momeneh Foroutan [aut], Yi Xie [aut], Ruqian Lyu [aut], Malvika Kharbanda [aut], Joseph Cursons [aut], Melissa J. Davis [aut]

SingscoreAMLMutations_1.28.0.tar.gz
SingscoreAMLMutations_1.28.0.zip(r-4.7-any)SingscoreAMLMutations_1.28.0.zip(r-4.6-any)SingscoreAMLMutations_1.28.0.zip(r-4.5-any)
SingscoreAMLMutations_1.28.0.tgz(r-4.6-any)SingscoreAMLMutations_1.28.0.tgz(r-4.5-any)
SingscoreAMLMutations_1.28.0.tar.gz(r-4.7-any)SingscoreAMLMutations_1.28.0.tar.gz(r-4.6-any)
SingscoreAMLMutations_1.28.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
SingscoreAMLMutations/json (API)

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

Bug tracker:https://github.com/davislaboratory/singscoreamlmutations/issues

Datasets:

On CRAN:

Conda:

geneexpressionworkflowgenomicvariantsworkflowimmunooncologyworkflowworkflow

2.00 score 1 stars 0 exports 156 dependencies

Last updated from:40a99957f9 (on RELEASE_3_23). Checks:1 NOTE, 7 WARNING, 1 ERROR, 1 OK. Indexed: no.
A new build is currently in progress.

TargetResultTimeFilesSyslog
bioc-checksNOTE237
linux-develWARNING436
source / vignettesERROR499
linux-releaseWARNING455
macos-releaseWARNING269
macos-oldrelWARNING353
windows-develWARNING346
windows-releaseWARNING245
windows-oldrelWARNING319
wasm-releaseOK201

Exports:

Dependencies:abindannotateAnnotationDbiaskpassbase64encBHBiobaseBiocFileCacheBiocGenericsBiocIOBiocParallelbiomaRtBiostringsbitbit64bitopsblobbslibcachemcigarillocirclizeclicliprcodetoolscolorspacecpp11crayoncrosstalkcurldata.tableDBIdbplyrdcanrDelayedArraydigestdoRNGdownloaderdplyredgeRevaluatefarverfastmapfilelockfontawesomeforeachformatRfsfutile.loggerfutile.optionsgenericsGenomicAlignmentsGenomicRangesggplot2ggrepelGlobalOptionsgluegraphgridExtraGSEABasegtablehighrhmshtmltoolshtmlwidgetshttrhttr2igraphIRangesisobanditeratorsjquerylibjsonliteKEGGRESTknitrlabelinglambda.rlaterlatticelazyevallifecyclelimmalocfitmagrittrMatrixMatrixGenericsmatrixStatsmclustmemoisemimeopensslorg.Hs.eg.dbotelpillarpkgconfigplotlyplyrpngprettyunitsprogresspromisespurrrR.methodsS3R.ooR.utilsR6rappdirsRColorBrewerRcppRCurlreadrreshapereshape2restfulrRhtslibrjsonrlangrmarkdownrngtoolsRsamtoolsRSQLitertracklayerrvestS4ArraysS4VectorsS7sassscalesselectrSeqinfoshapesingscoresnowSparseArraystatmodstringistringrSummarizedExperimentsysTCGAbiolinksTCGAbiolinksGUI.datatibbletidyrtidyselecttinytextzdbutf8vctrsviridisLitevroomwithrxfunXMLxml2xtableXVectoryaml