Alexander Lachmann

This is an issue with the ensembl annotation. Some genes do not have an official gene symbol. We use the ensembl id as a placeholder in this case.

you can use archs4py to mimic the output now

This code repository is somewhat out of date. You can check out the python package that can be used to work with archs4 data. The package also allows the local...

The pipeline is rewritten and iptimized, but the basic setup is similar to the one described in the paper.. The main difference is the updated genome annotation. This adds more...

Do you have any examples, so I can recreate the issue? If you have empty leading edges then I suspect there is some underlying issue. By definition, this should not...

I am closing the issue since this seems to be an extreme edge case. I have not encountered this behavior since. If it still persists I am happy to reopen...

I have not encountered this issue so far. I will keep a look-out. From the code, I don't see anything obvious. What system did this occur on?

Inf odds ratios are possible if the input gene set is a subset of a gene set in the gene set library. This is due to the formula given a...