New Format Converters in GenomeSpace

In response to user requests we have added the following three new format converters to the GenomeSpace ecosystem.

CDT to GCT converts the CDT (cluster data table) output file from GenePattern's HierarchicalClustering module to GenePattern's more widely used GCT format. The converter preserves identifiers and expression values and removes any column or row that maps clustering tree relationships.

CDT to TAB converts the CDT output file from GenePattern's HierarchicalClustering module to Genomica TAB format. As with the GCT conversion above, the converter preserves identifiers and expression values and removes any column or row that maps clustering tree relationships.

LST to geneset.TAB converts a Genomica LST file to the Genomica geneset.TAB format. The description column of the LST file is removed and the output file defines the LST file's column of gene symbols as a single gene set in a tab-delimited format. Define additional gene sets by manually revising the geneset.TAB file.

If you need additional format converters, please let us know at gs-help@broadinstitute.org.