Package: SingscoreAMLMutations 1.29.0

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_1.29.0.tar.gz
SingscoreAMLMutations_1.29.0.zip(r-4.7-any)SingscoreAMLMutations_1.29.0.zip(r-4.6-any)SingscoreAMLMutations_1.29.0.zip(r-4.5-any)
SingscoreAMLMutations_1.29.0.tgz(r-4.6-any)SingscoreAMLMutations_1.29.0.tgz(r-4.5-any)
SingscoreAMLMutations_1.29.0.tar.gz(r-4.7-any)SingscoreAMLMutations_1.29.0.tar.gz(r-4.6-any)
SingscoreAMLMutations_1.29.0.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.r-universe.dev', 'https://cloud.r-project.org'))

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

Datasets:

On BioConductor:SingscoreAMLMutations-1.29.0(workflows 3.24)SingscoreAMLMutations-1.28.0(workflows 3.23)

geneexpressionworkflowgenomicvariantsworkflowimmunooncologyworkflowworkflow

3.00 score 1 stars 4 scripts 0 exports 157 dependencies

Last updated from:933e8dab83. Checks:8 WARNING, 1 ERROR, 1 OK. Indexed: yes.

TargetResultTimeFilesSyslog
bioc-checksWARNING237
linux-develWARNING498
source / vignettesERROR517
linux-releaseWARNING448
macos-releaseWARNING382
macos-oldrelWARNING281
windows-develWARNING356
windows-releaseWARNING448
windows-oldrelWARNING306
wasm-releaseOK190

Exports:

Dependencies:abindannotateAnnotationDbiaskpassbase64encBHBiobaseBiocBaseUtilsBiocFileCacheBiocGenericsBiocIOBiocParallelbiomaRtBiostringsbitbit64bitopsblobbslibcachemcigarillocirclizeclicliprcodetoolscolorspacecpp11crayoncrosstalkcurldata.tableDBIdbplyrdcanrDelayedArraydigestdoRNGdownloaderdplyredgeRevaluatefarverfastmapfilelockfontawesomeforeachformatRfsfutile.loggerfutile.optionsgenericsGenomicAlignmentsGenomicRangesggplot2ggrepelGlobalOptionsgluegraphgridExtraGSEABasegtablehighrhmshtmltoolshtmlwidgetshttrhttr2igraphIRangesisobanditeratorsjquerylibjsonliteKEGGRESTknitrlabelinglambda.rlaterlatticelazyevallifecyclelimmalocfitmagrittrMatrixMatrixGenericsmatrixStatsmclustmemoisemimeopensslorg.Hs.eg.dbotelpillarpkgconfigplotlyplyrpngprettyunitsprogresspromisespurrrR.methodsS3R.ooR.utilsR6rappdirsRColorBrewerRcppRCurlreadrreshapereshape2restfulrRhtslibrjsonrlangrmarkdownrngtoolsRsamtoolsRSQLitertracklayerrvestS4ArraysS4VectorsS7sassscalesselectrSeqinfoshapesingscoresnowSparseArraystatmodstringistringrSummarizedExperimentsysTCGAbiolinksTCGAbiolinksGUI.datatibbletidyrtidyselecttinytextzdbutf8vctrsviridisLitevroomwithrxfunXMLxml2xtableXVectoryaml