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| estimate-package | ESTIMATE |
| common_genes | 10,412 common genes |
| estimate | ESTIMATE |
| estimateScore | Calculation of stromal, immune, and ESTIMATE scores |
| filterCommonGenes | Intersect input data with 10,412 common genes |
| outputGCT | Write gene expression data in GCT format |
| plotPurity | Plot tumor purity |
| PurityDataAffy | Affymetrix data |
| SI_geneset | two signatures for estimate |