Restoration of the Collapse function to GSEA Preranked.As a convenience, GSEA will continue to accept "true" and "false" as aliases for "Collapse" and "No_Collapse", respectively. The command-line parameters dealing with the Collapse function remain the same as before but now take these new option values use the GUI "Command" function to view examples of usage.Remap_Only is intended as a symbol conversion step and nothing more. The various collapse modes are ignored when remapping, and GSEA will report an error if the dataset contains multiple input symbols that map to the same gene in the specified CHIP file.The former true/false "Collapse dataset to gene symbols" parameter has been changed to "Collapse/Remap to gene symbols", with options "Collapse / No_Collapse / Remap_Only". Note that the UI around the Collapse function has changed to accommodate this new operation.See the MSigDB release notes for a discussion of recent changes to MSigDB symbol mapping procedures and our corresponding new recommendations for data set handling. Addition of gene identifier "Remap_Only" operation, to map datasets with older symbols to MSigDB's canonical namespace (Ensembl 97 in MSigDB 7.0).Addition of new Mean_of probes and Sum_of_probes collapse modes.Changed GSEA cache browsers to sort by date.Fixed a command-line option bug so the "-collapse" parameter is not required.Fixed CHIP parsing bugs related to empty values, whitespace, null, etc.
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