Tool: Use enrichr enrichment from command line
gravatar for WouterDeCoster
3.6 years ago by
WouterDeCoster44k wrote:

Yesterday I was reminded about a script I wrote a while ago, so might as well share it here. I wrote a command line script (python) to use Enrichr, based on their API and starting from their example code. So this isn't something very complicated or fancy, just convenient. I'm not affiliated to Enrichr. I just don't like leaving the command line and copy paste my gene list.

The script is available on github.
You can use it with a newline-separated list of gene symbols, or alternatively, it can read the list from stdin. This can be useful when piping the results of differential expression analysis or similar, just cut out the column containing gene symbols and pipe to the script. As of now it only accepts gene symbols and Enrichr is probably just for human genetics.

You can specify which database you want to query against, or just use a default set of databases. It's quite fast.
More detailed information is available in the README.

I welcome your feedback!

ADD COMMENTlink written 3.6 years ago by WouterDeCoster44k

It would be wonderful if you could also add plotting function ( to plot top terms ). I could work on it if you need help.

ADD REPLYlink written 3.6 years ago by geek_y11k

Hi Goutham Atla, sorry for the rather late response. But I guess that's justified these days. Creating plots of top terms sounds like a nice improvement, and if you got some ideas on how to implement that I certainly welcome your contribution!

ADD REPLYlink written 3.6 years ago by WouterDeCoster44k
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