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| 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 |