All functions

getPvals()

Estimate the empirical p-values

getStableGenes()

Get a list of stably expressed genes

generateNull()

Permutation test for the derived scores of each sample

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

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

simpleScore()

single-sample gene-set scoring method

multiScore()

single-sample gene-set scoring method for multiple signatures

singscore

singscore: A package for deriving gene-set scores at a single sample level

All 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