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