Where can we download the CCLE gene level count data (instead of TPM data currently provided by DepMap) with protein coding genes only?
The gene level counts are in
CCLE_RNAseq_reads_v2.csv and can be downloaded here. We don’t have a version with only protein coding genes. But you should be able to subset the genes accordingly.
Thanks for your reply. From the file description for the CCLE_RNAseq_read_v2_csv:
“RNAseq TPM gene expression data for just protein coding genes using RSEM. Log2 transformed, using a pseudo-count of 1”
It seems this file contains TPM data, not the count data.
I see the description you mentioned for
CCLE_RNAseq_read_v2_csv I see the following: “RNAseq read count data from RSEM”
Could you point me to where you see that description?
Sorry I clicked the data on the “Top Downloads” page therefore the description is for CCLE_expression_full_v2.csv. The description is right for CCLE_RNAseq_read_v2_csv file.