James Webber comments

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                                            James Webber

Failing with assertion error: "Gene and transcript records have unequal strands"...but they don't?

Can confirm that this runs successfully once I renamed the input gene/transcript IDs to something different. 👍 This did uncover another issue though: when creating the new GTF, IsoQuant will...

should extended_annotation.gtf be a superset of the input gtf?

I thought this was fixed, but I'm seeing some instances where the exon information for a gene was not copied over. I wonder if this is related to whether or...

should extended_annotation.gtf be a superset of the input gtf?

I noticed this initially in an unprocessed pseudogene (WASH7P) just because it happens to be very close to the beginning of `chr1`. So if there's any filtering based on biotype,...

should extended_annotation.gtf be a superset of the input gtf?

Ah! This probably a false alarm: it looks like the transcript name was not copied over, but the exons themselves are present. I was looking for the gene name and...

should extended_annotation.gtf be a superset of the input gtf?

The reason I noticed this is because I was looking at IGV, and it wasn't displaying the exons for WASH7P, only the gene body. I think this is really a...

Possible enhancement: multithreaded (via numba) mann-whitney tests

I haven't benchmarked against scanpy, only against `scipy.stats.mannwhitneyu` (which at this point can handle arrays, I know it couldn't before). On my laptop (an 8-core Intel MacBook Pro) it's about...

Fix error in paftools README.md

On this is a duplicate of #1239, didn't see it when I opened this.

Implement Layout Algorithms targeting Very Large Graphs

I find that SFDP is fast and works well for large graphs (10k to 100k nodes, for me), which is why I opened #917 way back in the day. A...

Call `numba.set_num_threads` when `n_jobs` is specified (e.g. in `scanpy.tl.rank_genes_group`)

Happy for you to do so! I only opened the issue as a suggestion as I didn't have time to make a PR myself.

Implementation of Louvain Algorithm

A general question: is the goal of `rustworkx` to include algorithms like this out-of-the-box, or would it be better to support third-party packages for things like this? I see that...