Rank-based single-sample gene set scoring method

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Documentation for package ‘singscore’ version 1.25.0

• 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