Datasets overview

[lgatto]

It would be useful to have a table (or list) with all the datasets, a short description and their dimensions.

[tfkillian]

A table of all current depmap package datasets has been added at the end of the Introduction section

[lgatto]

I didn't mean a long and exhaustive list of all packages and all versions, but rather a table that informs readers of the (types of) data they can get in the latest release. Something like:

Dataset	Description	Dimensions	Coverage	SourceVersion
crispr_20Q1	(CERES) Batch and off-target corrected CRISPR-Cas9 gene knockdout dependency data	18333 genes, 739 cell lines	29 primary diseases and 26 lineages	Feb 20 2019
copyNumber_20Q1	WES log copy number data	27639 genes, 1713 cell lines	35 primary diseases and 36 lineages	Feb 20 2019
TPM_20Q1	CCLE TPM RNAseq gene expression data for protein coding genes	19144 genes, 1270 cancer cell lines	32 primary diseases and 34 lineages	Feb 20 2019
mutationCalls_20Q1	Merged mutation calls (for coding region, germline filtered) and includes data	18802 genes, 1697 cell lines	35 primary diseases and 36 lineages	Feb 20 2019
metadata_20Q1	Metadata for cell lines in the 20Q1 DepMap release	1775 cell lines	35 primary diseases and 37 lineages	Feb 20 2019

which I can generate from the csv file. But

• I assume you created that table using a script? It so, could you add it (named depmap_datasets_list.R)
• Should the dates not be Feb 2020?

[tfkillian]

I have pushed at update to the paper so that the table has been condensed to reflect the most recently available datasets for each type (similar to that shown above, but also showing RPPA_19Q3, rnai_19Q3 and drug_sensitivity_19Q3)

I did not create the tables from a script, I created them in Excel by manually scraping the content from the wed and collating our existing metadata files for each release. I have also corrected the erroneous Feb 2019 release date.

[lgatto]

Thanks.