-
Notifications
You must be signed in to change notification settings - Fork 3
New issue
Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.
By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.
Already on GitHub? Sign in to your account
Compute enrichment of gene sets in our predictions #6
Comments
Let us catalogue gene sets here. We need to download each one (see #5) and add it to the enrichment analysis.
|
Currently the downloadable gmt file available for the COVID-19 Crowd Generated Gene sets does not have the main descriptor text of the gene set in the file, making most gene sets unidentifiable. I made an issue on their repo (#82) asking them to fix it. |
They fixed the gmt file for the COVID-19 Crowd Generated Gene! |
of the top predictions of each algorithm, and of any given gene set. Currently only tests GO BP, MF, and CC. Issue #6
of the top predictions of each algorithm, and of any given gene set. Currently only tests GO BP, MF, and CC. Issue #6
@jlaw9 @n-tasnina what is the status of running our enrichment pipeline on the COVID-19 gene sets? |
We have the COVID-19 gene sets in GMT format, just need to update our scripts to test for enrichment of them. Here's the clusterProfiler documentation for our own gene sets. |
Yeah, sure.I will add a function in enrichment.py to do this.
…On Fri, May 22, 2020, 2:27 PM Jeff Law ***@***.***> wrote:
We have the COVID-19 gene sets in GMT format, just need to update our
scripts to test for enrichment of them. Here's the clusterProfiler
documentation for our own gene sets
<https://guangchuangyu.github.io/2015/05/use-clusterprofiler-as-an-universal-enrichment-analysis-tool/>
.
@n-tasnina <https://github.com/n-tasnina> can you add a function for that
in our enrichment.py?
—
You are receiving this because you were mentioned.
Reply to this email directly, view it on GitHub
<#6 (comment)>,
or unsubscribe
<https://github.com/notifications/unsubscribe-auth/ANSAMM23BOLFRTZ2HLHTQ7LRS272RANCNFSM4LZYUK7A>
.
|
We can close this issue as well. Here is the link to the python script where we did enrichment analysis. |
We have a ranked list of predictions coming from network propagation or from host-virus PPI prediction. This issue is relevant mainly for human proteins. We also have a set of gene sets, e.g., from https://amp.pharm.mssm.edu/covid19/. We want to assess to what extent each gene set is enriched in our list of predictions.
There are two approaches I suggest:
We must correct for testing multiple hypotheses.
The text was updated successfully, but these errors were encountered: