Treehouse compendium of RNA-Seq gene expression data from tumors

We uniformly analyze sequence data to generate a resource for comparative gene expression studies Gene expression data for 11,454 tumor samples gathered from different sources and consistently processed across all samples. Data pocessing steps were as follows: Adapters are removed with CutAdapt v1.9 ​(Martin, 2011)​ Reads are aligned by STAR v 2.4.2a using indices generated from the human reference genome GRCh38 and the human gene models Gencode 23 ​(Dobin et al., 2013) RSEM 1.2.25 is used to quantify gene expression ​(Li and Dewey, 2011)​. Gene level expression in TPM is log transformed: log2(TPM+1)