Easy single cell analysis platform for enrichment

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Documentation for package ‘escape’ version 1.12.0

• DESCRIPTION file.
• User guides, package vignettes and other documentation.
• Package NEWS.

Help Pages

calculate_Uscore	Calculate rankings and scores for query data and given signature set
check_genes	Check if all genes in signatures are found in data matrix - otherwise add zero counts in data-matrix to complete it
check_signature_names	Check signature names and add standard names is missing
data_to_ranks_data_table	Calculate per-cell feature rankings
enrichIt	Calculate gene set enrichment scores for single-cell data
enrichmentPlot	Gene Rank Enrichment Plot Display the rank order density for individual gene sets by group identify. This function will use the group variable to take the mean rank order across all individual cells.
escape.gene.sets	In-Built Gene Sets for Escape
getGeneSets	Get a collection of gene sets to perform enrichment on
getSignificance	Perform significance testing between groups and enrichement scores.
masterPCAPlot	Visualize the components of the PCA analysis of the enrichment results
pcaEnrichment	Density plot of the principal components
performPCA	Calculate Principal Components for the Enrichment Scores
rankings2Uscore	Get signature scores from pre-computed rank matrix
ridgeEnrichment	Generate a ridge plot to examine enrichment distributions
ScoreSignatures_UCell	Calculate module enrichment scores from single-cell data
splitEnrichment	Generate a split violin plot examine enrichment distributions
StoreRankings_UCell	Calculate and store gene rankings for a single-cell dataset
u_stat	Calculate Mann Whitney U from a vector of ranks
u_stat_signature_list	Calculate U scores for a list of signatures, given a rank matrix