Jeff Hammerbacher
Jeff Hammerbacher
Algolia has changed the DocSearch program and it's going to require some code changes on our side. [Gmail - Fwd_ The DocSearch team have some exciting news for you!.pdf](https://github.com/pystatgen/sgkit/files/7785120/Gmail.-.Fwd_.The.DocSearch.team.have.some.exciting.news.for.you.pdf)
When converting large VCF files with `vcf_to_zarr`, it would be nice to display a progress bar to users.
@eric-czech has a nice collection of notebooks exploring real, open canine data, including phenotypes, at https://github.com/related-sciences/gwas-analysis/tree/master/notebooks/organism/canine. It might make sense to port these notebooks to `sgkit`.
Given the philosophy of `sgkit` to rely on PyData APIs when possible, I thought it might be nice to have a notebook that spends time introducing and exploring PyData projects...
I had to get rid of `fastmath=True` param from `guvectorize` due to [this issue](https://github.com/numba/numba/issues/2919) in Numba. _Originally posted by @aktech in https://github.com/pystatgen/sgkit/issues/306#issuecomment-711432004_
While working on #504 I noticed a few things that make the docs look cleaner, in my opinion. I'm curious to hear from others. - [ ] Remove `Indices and...
A reminder to myself to do this some time soon so we can shut down Discourse. - [ ] [Top posts](https://discourse.pystatgen.org/latest?order=views) - [ ] Update [contributing.rst](https://github.com/pystatgen/sgkit/blob/main/docs/contributing.rst) to point to GitHub...
### Discussed in https://github.com/pystatgen/sgkit/discussions/652 Originally posted by **patrick-koenig** August 19, 2021 Hi sgkit team, is it planned to port the GFF3 I/O utility methods (especially the gff3_to_dataframe() method) of scikit-allel...
We should collect weird VCFs and ensure we parse them correctly. It would be nice if this zoo had metadata about what's interesting about a file. @jeromekelleher can you point...
Motivated by @hyanwong at https://github.com/pystatgen/sgkit/discussions/580 Some popgen methods need to know which allele at each site is the ancestral allele (cf. https://biology.stackexchange.com/questions/19159/ancestral-allele-explanation). We should augment our data model to optionally...