extracting a gene from a gmt file
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10 weeks ago
Bogdan ★ 1.1k

Dear all,

starting from a conversation at : https://bioinformatics.stackexchange.com/questions/5400/how-to-convert-data-in-gmt-format-to-dataframe, would you please advice :

given a gmt file, how could extract the pathways that are associated with a specific gene ?

thank you very much !

Bogdan

a gene many extract pathways with associated • 254 views
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10 weeks ago
Sam ★ 3.8k

Considering the format of the gmt file, I guess the easiest way will be to do

grep -f <file with gene> -w <gmt file>
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