All functions
|
getPvals()
|
Estimate the empirical p-values |
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 |