|Score a region set using feature contribution scores
|Score many region sets
|Atf3 binding regions.
|A GRanges object with coordinates for select BRCA ATAC-seq...
|A matrix with ATAC-seq counts in select peak regions from...
|A GRanges object with genomic coordinates for cytosines from...
|A data.frame with patient metadata for breast cancer...
|A matrix with DNA methylation levels from some CpGs on...
|A matrix with principal component scores for PCs 1-4 for four...
|A data.frame with principal component scores for PCs 1-4 for...
|Coordinate Covariation Analysis (COCOA)
|Converts COCOA permutation results to null distributions and...
|Estrogen receptor alpha binding regions.
|Gata3 binding regions.
|Get a p-value for region set scores based on a gamma...
|Create a "meta-region" profile
|Get p-value or z-score based on permutation results
|Get regions that are most associated with target variable
|Nrf1 binding regions.
|Plot ranked region set scores, annotating groups of interest
|Visualize how individual regions are associated with target...
|Get indices for top scored region sets
|Heatmap of region set scores
|Example COCOA Results (made up)
|Run COCOA: quantify inter-sample variation, score region sets
|Run COCOA permutations to get p-values
|Visualize how genomic signal in a region set changes along a...
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