Where can I find detailed documentation on your bioinformatic pipelines used for computing the copy number ratios, gene expression, and mutation calls?

You can find more details on the methods, including pipelines, in Supplementary Information section of the CCLE papers. Older files are described in the original CCLE manuscript and newer files are described in the new CCLE manuscript. Additional information can also be found in the README.txt file for each DepMap Release.