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Issues list

Consider standardizing the API of pca and pc_relate question Further information is requested
#1077 opened Apr 27, 2023 by timothymillar
4 👍 3
Write pedigree data to VCF IO Issues related to reading and writing common third-party file formats
#1014 opened Jan 30, 2023 by timothymillar
👍 2
Comparing datasets - remapping alleles.
#1099 opened Jun 29, 2023 by benjeffery
👍 2
docker image
#770 opened Nov 19, 2021 by elswob
4 👍 2
Move to NumPy's ArrayLike and DtypeLike process + tools
#452 opened Feb 3, 2021 by tomwhite
👍 2
Enable indexing on datasets by default data representation Issues related to how data is represented: data types, data structures, indexes, access methods, etc
#473 opened Mar 2, 2021 by tomwhite
5 👍 2
Unused alleles being "" is confusing for downstream tools - consider None?
#1006 opened Jan 25, 2023 by benjeffery
12 👍 1
Harness CUDA's shared memory to speed up GPU calculations
#517 opened Apr 6, 2021 by aktech
👍 1
Remove contigs dataset attribute data representation Issues related to how data is represented: data types, data structures, indexes, access methods, etc IO Issues related to reading and writing common third-party file formats
#1058 opened Apr 5, 2023 by tomwhite
👍 1
Track and improve the performance of allele counting method core operations Issues related to domain-specific functionality such as LD pruning, PCA, association testing, etc. performance
#49 opened Jul 16, 2020 by eric-czech
7 👍 1
Compute LD scores
#441 opened Jan 17, 2021 by hammer
👍 1
Investigate ragged arrays to represent alleles data representation Issues related to how data is represented: data types, data structures, indexes, access methods, etc
#634 opened Jul 19, 2021 by tomwhite
6 👍 1
Roadmap documentation Improvements or additions to documentation
#564 opened May 13, 2021 by jeromekelleher
👍 1
Document reading tabular pedigree formats into sgkit documentation Improvements or additions to documentation IO Issues related to reading and writing common third-party file formats
#1012 opened Jan 30, 2023 by timothymillar
3 👍 1
Add benchmark suite performance process + tools
#68 opened Jul 27, 2020 by eric-czech
1 task
6 👍 1
Copy contigs from attribute to array in load_dataset IO Issues related to reading and writing common third-party file formats
#1057 opened Apr 5, 2023 by tomwhite 0.9.1
@benjeffery
👍 1
Create a public GWAS workflow for collaborative optimization
#438 opened Jan 13, 2021 by eric-czech
10 👍 1
Add variant annotation functions core operations Issues related to domain-specific functionality such as LD pruning, PCA, association testing, etc.
#112 opened Aug 13, 2020 by eric-czech
4 👍 1
Example popgen notebook documentation Improvements or additions to documentation
#602 opened Jun 8, 2021 by tomwhite
@tomwhite
7 👍 1
Remove mention of CuPy in docs documentation Improvements or additions to documentation
#579 opened May 23, 2021 by hammer
👍 1
Read pedigree data from VCF IO Issues related to reading and writing common third-party file formats
#1013 opened Jan 30, 2023 by timothymillar
1 👍 1
import sgkit takes ~1.5s
#931 opened Oct 14, 2022 by benjeffery
7 👍 1
Logging from vcf_to_zarr enhancement New feature or request
#910 opened Sep 23, 2022 by jeromekelleher
2 👍 1
Compute polygenic risk scores with sgkit
#279 opened Sep 24, 2020 by hammer
7 👍 1
Implement G123 selection statistic
#980 opened Dec 20, 2022 by sanjaynagi
8 👍 1
ProTip! Updated in the last three days: updated:>2024-07-15.