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| GSA | Gene set analysis |
| GSA.correlate | "Correlates" a gene set collection with a given list of gene nams |
| GSA.func | Gene set analysis without permutations |
| GSA.genescores | Individual gene scores from a gene set analysis |
| GSA.listsets | List the results from a Gene set analysis |
| GSA.make.features | Creates features from a GSA analysis that can be used in other procedures |
| GSA.plot | Plot the results from a Gene set analysis |
| GSA.read.gmt | Read in a gene set collection from a .gmt file |