calcGseaStat |
Calculates GSEA statistics for a given query gene set |
calcGseaStatBatchCpp |
Calculates GSEA statistic valus for all gene sets in 'selectedStats' list. |
collapsePathways |
Collapse list of enriched pathways to independent ones. |
examplePathways |
Example list of mouse Reactome pathways. |
exampleRanks |
Example vector of gene-level statistics obtained for Th1 polarization. |
fgsea |
Runs preranked gene set enrichment analysis. |
fgseaLabel |
Runs label-permuring gene set enrichment analysis. |
fgseaMultilevel |
Runs preranked gene set enrichment analysis. |
fgseaSimpleImpl |
Runs preranked gene set enrichment analysis for preprocessed input data. |
gmtPathways |
Returns a list of pathways from a GMT file. |
multilevelError |
Calculates the expected error for the standard deviation of the P-value logarithm. |
multilevelImpl |
Calculates P-values for preprocessed data. |
plotEnrichment |
Plots GSEA enrichment plot. |
plotGseaTable |
Plots table of enrichment graphs using ggplot and gridExtra. |
reactomePathways |
Returns a list of Reactome pathways for given Entrez gene IDs |