Package: singscore 1.27.0

Malvika Kharbanda

singscore: Rank-based single-sample gene set scoring method

A simple single-sample gene signature scoring method that uses rank-based statistics to analyze the sample's gene expression profile. It scores the expression activities of gene sets at a single-sample level.

Authors:Dharmesh D. Bhuva [aut], Ruqian Lyu [aut, ctb], Momeneh Foroutan [aut, ctb], Malvika Kharbanda [aut, cre]

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singscore.pdf |singscore.html✨
singscore/json (API)
NEWS

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

Peer review:

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

Pkgdown:https://davislaboratory.github.io

Datasets:
  • scoredf_ccle_epi - Pre-computed scores of the CCLE dataset against an epithelial gene signature
  • scoredf_ccle_mes - Pre-computed scores of the CCLE dataset against a mesenchymal gene signature
  • scoredf_tcga_epi - Pre-computed scores of the TCGA breast cancer gene expression matrix against an epithelial signature
  • scoredf_tcga_mes - Pre-computed scores of the TCGA breast cancer gene expression matrix against a mesenchymal signature
  • tgfb_expr_10_se - An example gene expression dataset
  • tgfb_gs_dn - Gene set of down-regulated genes for the TGFb-induced EMT gene signature
  • tgfb_gs_up - Gene set of up-regulated genes for the TGFb-induced EMT gene signature
  • toy_expr_se - A toy gene expression dataset of two samples
  • toy_gs_dn - A gene set object of down-regulated genes for the toy dataset
  • toy_gs_up - A gene set object of up-regulated genes for the toy dataset

On BioConductor:singscore-1.27.0(bioc 3.21)singscore-1.26.0(bioc 3.20)

softwaregeneexpressiongenesetenrichmentbioinformatics

9.88 score 40 stars 3 packages 117 scripts 2.3k downloads 13 mentions 11 exports 119 dependencies

Last updated 2 months agofrom:b18b6f0c6f. Checks:OK: 1 NOTE: 6. Indexed: yes.

TargetResultDate
Doc / VignettesOKNov 30 2024
R-4.5-winNOTENov 30 2024
R-4.5-linuxNOTENov 30 2024
R-4.4-winNOTENov 30 2024
R-4.4-macNOTENov 30 2024
R-4.3-winNOTENov 30 2024
R-4.3-macNOTENov 30 2024

Exports:generateNullgetPvalsgetStableGenesmultiScoreplotDispersionplotNullplotRankDensityplotScoreLandscapeprojectScoreLandscaperankGenessimpleScore

Dependencies:abindannotateAnnotationDbiaskpassbase64encBHBiobaseBiocGenericsBiocParallelBiostringsbitbit64blobbslibcachemclicodetoolscolorspacecpp11crayoncrosstalkcurldata.tableDBIDelayedArraydigestdplyredgeRevaluatefansifarverfastmapfontawesomeformatRfsfutile.loggerfutile.optionsgenericsGenomeInfoDbGenomeInfoDbDataGenomicRangesggplot2ggrepelgluegraphGSEABasegtablehighrhtmltoolshtmlwidgetshttrIRangesisobandjquerylibjsonliteKEGGRESTknitrlabelinglambda.rlaterlatticelazyevallifecyclelimmalocfitmagrittrMASSMatrixMatrixGenericsmatrixStatsmemoisemgcvmimemunsellnlmeopensslpillarpkgconfigplogrplotlyplyrpngpromisespurrrR6rappdirsRColorBrewerRcppreshapereshape2rlangrmarkdownRSQLiteS4ArraysS4VectorssassscalessnowSparseArraystatmodstringistringrSummarizedExperimentsystibbletidyrtidyselecttinytexUCSC.utilsutf8vctrsviridisLitewithrxfunXMLxtableXVectoryamlzlibbioc

singscore

Ruqian Lyu

Rendered fromsingscore.Rmdusingknitr::rmarkdownon Nov 30 2024.

Last update: 2022-05-12
Started: 2017-11-15

Readme and manuals

Help Manual

Help pageTopics
Permutation test for the derived scores of each samplegenerateNull generateNull,GeneSet,ANY-method generateNull,GeneSet,GeneSet-method generateNull,vector,ANY-method generateNull,vector,vector-method
Estimate the empirical p-valuesgetPvals
Get a list of stably expressed genesgetStableGenes
single-sample gene-set scoring method for multiple signaturesmultiScore multiScore,matrix,GeneSetCollection,GeneSetCollection-method multiScore,matrix,GeneSetCollection,missing-method multiScore,matrix,list,list-method multiScore,matrix,list,missing-method
Plot the score v.s. despersion for all samplesplotDispersion
Plot the empirically estimated null distribution and associated p-valuesplotNull
Plot the densities of ranks for one sampleplotRankDensity plotRankDensity,ANY,GeneSet,GeneSet-method plotRankDensity,ANY,GeneSet,missing-method plotRankDensity,ANY,vector,missing-method plotRankDensity,ANY,vector,vector-method
Plot landscape of two gene signatures scoresplotScoreLandscape
Project data on the landscape plot obtained from 'plotScoreLandscape()'projectScoreLandscape
Rank genes by the gene expression intensitiesrankGenes rankGenes,data.frame-method rankGenes,DGEList-method rankGenes,ExpressionSet-method rankGenes,matrix-method rankGenes,SummarizedExperiment-method
Pre-computed scores of the CCLE dataset against an epithelial gene signaturescoredf_ccle_epi
Pre-computed scores of the CCLE dataset against a mesenchymal gene signaturescoredf_ccle_mes
Pre-computed scores of the TCGA breast cancer gene expression matrix against an epithelial signaturescoredf_tcga_epi
Pre-computed scores of the TCGA breast cancer gene expression matrix against a mesenchymal signaturescoredf_tcga_mes
single-sample gene-set scoring methodsimpleScore simpleScore,matrix,GeneSet,GeneSet-method simpleScore,matrix,GeneSet,missing-method simpleScore,matrix,vector,missing-method simpleScore,matrix,vector,vector-method
singscore: A package for deriving gene-set scores at a single sample levelsingscore
An example gene expression datasettgfb_expr_10_se
Gene set of down-regulated genes for the TGFb-induced EMT gene signaturetgfb_gs_dn
Gene set of up-regulated genes for the TGFb-induced EMT gene signaturetgfb_gs_up
A toy gene expression dataset of two samplestoy_expr_se
A gene set object of down-regulated genes for the toy datasettoy_gs_dn
A gene set object of up-regulated genes for the toy datasettoy_gs_up