Ryan Dale

icon location Bethesda, MD

Results 126 comments of Ryan Dale

Update edgeR version

@claire-prince we need to wait for conda-forge to finish their R 4.2 migration before we can start on bioconductor, unfortunately.

Update AmpliGone recipe for version 1.1.0

@BiocondaBot please merge

Better handling of merged components

@innovate-invent, please reopen (and include a concrete example I could use to test) if this is still an issue.

introns = G.interfeatures(exons) gives 0 introns. is it because exon gives unnamed_exon?

@jekang39, please reopen this (and include some example data) if this is still an issue.

sample snippet for the ChIP signal visualization?

That's correct, metaseq does not know anything about gene locations. You might want to give deepTools a try, since it is better maintained than metaseq. It is also written in...

Add support for csi index

Thanks! Can you please add a test to this PR?

create_db() does not parse directives from GFF files starting in v0.11.0

@dtdoering I'm unable to reproduce in a test -- see the new test at https://github.com/daler/gffutils/pull/221/commits/a4b443b1eb8f9c17d2b6664f9c63f53b8b1cb0a9 and passing tests [here](https://github.com/daler/gffutils/actions/runs/5454412144/jobs/9924498260?pr=221). Are you able to reproduce this with the latest in the...

Example1 problem #2

Thanks for reporting. Unfortunately, I'm unable to reproduce the issue. For troubleshooting, can you please try setting `processes = 1` and then re-run to get a more informative error message.

Example1 problem #2

There are multiple calls in that chunk, and it looks like you only changed the second one. How about just running this: ```python ip_array = ip_signal.array( tsses_1kb, bins=100, processes=1) ```

Example1 problem #2

Can you try the same with `processes=None` please?