omniphenotype

Code for the Cell fitness is an omniphenotype paper. Current version, v5, is available on BioRxiv.

Code to generate data for each figure was written in python, R, Perl, PHP, or MySQL. The underlying data can be accessed as described in the methods.

Figure 1

• NIH grant data is available to download from the NIH RePORTER website.
• Huttlin (Bioplex) data is available to download from their website.
• Figure 1.R has code to intersect this data with that of the DepMap.

Figure 3

• figure3A.sql has multiple MySQL commands that are needed to generate the data shown in Figure 3A.

• Any gene cluster can be input into the figure3B.py script to yield the data that can be converted into the volcano plot as shown in Figure 3B.

• Figure 3B statistics (enrichment analysis) was performed using SciPy. The code is available via here.

Figure 4

• For the common disease restricted analysis in Figure S1, preceeding this analysis, we dumped all of PubMed into a MySQL database table, which we then queried for the co-occurrence of {gene} AND {condition}.

Figure 5

• Guzzle, which is a PHP library to make HTTP requests, is required to run Figure 5 code.