# Rank-based single-sample gene set scoring method

## Documentation for package ‘singscore’ version 1.20.0

- DESCRIPTION file.
- User guides, package vignettes and other documentation.
- Package NEWS.

## Help Pages

generateNull | Permutation test for the derived scores of each sample
generateNull-method | Permutation test for the derived scores of each sample
getPvals | Estimate the empirical p-values
getStableGenes | Get a list of stably expressed genes
multiScore | single-sample gene-set scoring method for multiple signatures
multiScore-method | single-sample gene-set scoring method for multiple signatures
plotDispersion | Plot the score v.s. despersion for all samples
plotNull | Plot the empirically estimated null distribution and associated p-values
plotRankDensity | Plot the densities of ranks for one sample
plotRankDensity-method | Plot the densities of ranks for one sample
plotScoreLandscape | Plot landscape of two gene signatures scores
projectScoreLandscape | Project data on the landscape plot obtained from 'plotScoreLandscape()'
rankGenes | Rank genes by the gene expression intensities
rankGenes-method | Rank genes by the gene expression intensities
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
simpleScore | single-sample gene-set scoring method
simpleScore-method | single-sample gene-set scoring method
singscore | singscore: A package for deriving gene-set scores at a single sample level
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