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Apply a Gating-ML 2.0 file on an FCS data file (gate and/or transform list mode data)

Generate .cls file(s) from a hierarchical clustering result. This works on R-2.5. For another version, clone it and edit <R2.5> in Command field.

Compute detection p-values for gene-expression microarray data. If you need to specify R, clone it and modify Command Line <R> like <R2.5> to match your version.

FCSClean v16

Clean up an FCS file by marking events affected by problems during data acquisition

GCTforIGV v2.4

Format a GCT file to be readable by the Integrative Genome Viewer (IGV).

Apply a log base 2 transformation to data from a GCT file.

Apply a (quantile, scale, or Znorm) normalization on a GCT file.

ReorderGCT v6.4

Reorder a GCT by sorting on a property such as the gene symbol, average expression level, sum and variance

TCGA.Merge - version 1

@GPArchive