Package: singscore 1.33.0

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]

singscore_1.33.0.tar.gz
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manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
singscore/json (API)

# Install 'singscore' in R:

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

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

Pkgdown/docs site: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-1.33.0(bioc 3.24)singscore-1.32.0(bioc 3.23)

software geneexpression genesetenrichment bioinformatics

10.42 score 49 stars 6 packages 186 scripts 13 mentions 11 exports 111 dependencies

Last updated from:f3f58b9da9. Checks:8 NOTE, 2 OK. Indexed: yes.

Target	Result	Time
bioc-checks	NOTE	175
linux-devel-x86_64	NOTE	430
source / vignettes	OK	305
linux-release-x86_64	NOTE	374
macos-release-arm64	NOTE	209
macos-oldrel-arm64	NOTE	191
windows-devel	NOTE	303
windows-release	NOTE	272
windows-oldrel	NOTE	271
wasm-release	OK	197

Exports:generateNull getPvals getStableGenes multiScore plotDispersion plotNull plotRankDensity plotScoreLandscape projectScoreLandscape rankGenes simpleScore

Dependencies:abind annotate AnnotationDbi askpass base64enc BH Biobase BiocGenerics BiocParallel Biostrings bit bit64 blob bslib cachem cli codetools cpp11 crayon crosstalk curl data.table DBI DelayedArray digest dplyr edgeR evaluate farver fastmap fontawesome formatR fs futile.logger futile.options generics GenomicRanges ggplot2 ggrepel glue graph GSEABase gtable highr htmltools htmlwidgets httr IRanges isoband jquerylib jsonlite KEGGREST knitr labeling lambda.r later lattice lazyeval lifecycle limma locfit magrittr Matrix MatrixGenerics matrixStats memoise mime openssl otel pillar pkgconfig plotly plyr png promises purrr R6 rappdirs RColorBrewer Rcpp reshape reshape2 rlang rmarkdown RSQLite S4Arrays S4Vectors S7 sass scales Seqinfo snow SparseArray statmod stringi stringr SummarizedExperiment sys tibble tidyr tidyselect tinytex utf8 vctrs viridisLite withr xfun XML xtable XVector yaml

singscore

Rendered fromsingscore.Rmdusingknitr::rmarkdown

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

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
Permutation test for the derived scores of each sample	generateNull generateNull,GeneSet,ANY-method generateNull,GeneSet,GeneSet-method generateNull,vector,ANY-method generateNull,vector,vector-method
Estimate the empirical p-values	getPvals
Get a list of stably expressed genes	getStableGenes
single-sample gene-set scoring method for multiple signatures	multiScore 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 samples	plotDispersion
Plot the empirically estimated null distribution and associated p-values	plotNull
Plot the densities of ranks for one sample	plotRankDensity 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 scores	plotScoreLandscape
Project data on the landscape plot obtained from 'plotScoreLandscape()'	projectScoreLandscape
Rank genes by the gene expression intensities	rankGenes 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 signature	scoredf_ccle_epi
Pre-computed scores of the CCLE dataset against a mesenchymal gene signature	scoredf_ccle_mes
Pre-computed scores of the TCGA breast cancer gene expression matrix against an epithelial signature	scoredf_tcga_epi
Pre-computed scores of the TCGA breast cancer gene expression matrix against a mesenchymal signature	scoredf_tcga_mes
single-sample gene-set scoring method	simpleScore 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 level	singscore-package singscore
An example gene expression dataset	tgfb_expr_10_se
Gene set of down-regulated genes for the TGFb-induced EMT gene signature	tgfb_gs_dn
Gene set of up-regulated genes for the TGFb-induced EMT gene signature	tgfb_gs_up
A toy gene expression dataset of two samples	toy_expr_se
A gene set object of down-regulated genes for the toy dataset	toy_gs_dn
A gene set object of up-regulated genes for the toy dataset	toy_gs_up