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[xiang...@scilifelab.se]

Dear iLINCS Team,

I am trying to download the LINCS consensus gene (CGS) knockdown signatures data in iLINCS website. It seems i can only download the metadata such as signature ID , Perturbagen and cell line. But how can I download the differential gene expressions and p-values for 978 Landmark Genes for all the cell lines in bulk?

By the way, are the inferred measurements of differential gene expressions for other genes for each perturbagen released? When is it available?

Many thanks!

[mbfazel]

Hi Xiangyu,

There are two options you can download signature data from ilincs.

1- From ilincs website: you need to select the signatures you want to download (Not more than 500 at a time though) by selecting individually or "Selection" dropdown button (image bellow) and then "Download signature (xls)" or "Download signature (gct)" format from "Download" drop down button.

2- You can also use ilincs APIs at https://github.com/uc-bd2k/ilincsAPI/blob/master/usingIlincsApis.Rmd to do the same thing. 

Just look for "downloadSignature" in the scripts and follow the instructions.

Hope it helps,

Mehdi