Package: singscore 1.25.0

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'))

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

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-1.25.0(bioc 3.20)singscore-1.24.0(bioc 3.19)

bioconductor-package

11 exports 1.45 score 119 dependencies 2 dependents 13 mentions

Last updated 2 months agofrom:7eeaa470aa

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 colorspace cpp11 crayon crosstalk curl data.table DBI DelayedArray digest dplyr edgeR evaluate fansi farver fastmap fontawesome formatR fs futile.logger futile.options generics GenomeInfoDb GenomeInfoDbData 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 MASS Matrix MatrixGenerics matrixStats memoise mgcv mime munsell nlme openssl pillar pkgconfig plogr plotly plyr png promises purrr R6 rappdirs RColorBrewer Rcpp reshape reshape2 rlang rmarkdown RSQLite S4Arrays S4Vectors sass scales snow SparseArray statmod stringi stringr SummarizedExperiment sys tibble tidyr tidyselect tinytex UCSC.utils utf8 vctrs viridisLite withr xfun XML xtable XVector yaml zlibbioc

singscore

Ruqian Lyu

Rendered fromsingscore.Rmdusingknitr::rmarkdownon Jun 27 2024.

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
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