scverse/gget

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🧬 gget enables efficient querying of genomic reference databases

Stars: 1.2k
Forks: 97
Open beginner issues: 0
Indexed issues: 25

Dominant language: Python
License: BSD-2-Clause
Last GitHub push: Sep 18, 2026
Latest indexed: Sep 19, 2026
Contributing guide: Contributing guide
Code of conduct: Code of conduct
Beginner labels: No beginner labels indexed
PR merge metrics: No merged PRs in 30d

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25 open issues indexed

CI: `test_info_gene` is flaky — exact-match assertion over best-effort UniProt/NCBI enrichment Open

Difficulty 2/5 1-3 hours Newbie friendliness 78/100

scverse/gget#267 · 1 comment · Opened Jul 12, 2026
CI: `test_cellxgene_adata` fails — cellxgene-census AnnData now exposes a `layers` entry (live-data drift) Open

Difficulty 2/5 1-3 hours Newbie friendliness 74/100

scverse/gget#265 · Opened Jul 8, 2026
`gget setup alphafold` / `gget alphafold` break against the current `deepmind/alphafold` main branch Open

Difficulty 4/5 3-5 days Newbie friendliness 45/100

scverse/gget#264 · Opened Jul 7, 2026
gget archs4 uses the legacy maayanlab.cloud endpoint; ARCHS4 has moved to archs4.org (evaluate migration, low priority) Open

Difficulty 5/5 Over a week Newbie friendliness 35/100

scverse/gget#254 · Opened Jun 26, 2026
Replace cellxgene-census Open

Difficulty 4/5 3-5 days Newbie friendliness 35/100

scverse/gget#218 · 1 comment · Opened Jun 12, 2026
Add typing & type checking Open

Difficulty 4/5 3-5 days Newbie friendliness 42/100

scverse/gget#216 · 3 comments · Opened Jun 11, 2026
gget virus: add function to only download new sequences Open

enhancement

Difficulty 5/5 Over a week Newbie friendliness 25/100

scverse/gget#204 · Opened Feb 5, 2026
Support core_nt database in blast module Open

enhancement

Difficulty 2/5 1-3 hours Newbie friendliness 45/100

scverse/gget#188 · Opened Nov 20, 2025
gget seq ENST... gets genomic sequences (exons+introns) instead of transcript sequences Open

Difficulty 3/5 1-2 days Newbie friendliness 45/100

scverse/gget#187 · Opened Oct 16, 2025
gget ref assembly report Open

enhancement

Difficulty 4/5 3-5 days Newbie friendliness 25/100

scverse/gget#179 · 1 comment · Opened May 16, 2025
Support download of PDBx/mmCIF format files in gget pdb (legacy PDB format will be phased out) Open

enhancement

Difficulty 3/5 1-2 days Newbie friendliness 35/100

scverse/gget#178 · Opened May 1, 2025
gget opentargets -r diseases Open

Difficulty 4/5 3-5 days Newbie friendliness 25/100

scverse/gget#168 · 1 comment · Opened Nov 18, 2024
Add modules to interface with new projects from the Enrichr/Archs4 group Open

enhancement

Difficulty 4/5 3-5 days Newbie friendliness 35/100

scverse/gget#164 · 1 comment · Opened Oct 2, 2024
Alliance Genome Resources Open

enhancement

Difficulty 5/5 Over a week Newbie friendliness 25/100

scverse/gget#162 · Opened Sep 29, 2024
Pineapple module to download bio-imaging data Open

enhancement

Difficulty 4/5 3-5 days Newbie friendliness 35/100

scverse/gget#161 · Opened Sep 27, 2024
ENCODE downloader Open

enhancement

Difficulty 5/5 Over a week Newbie friendliness 35/100

scverse/gget#151 · 3 comments · Opened Jul 6, 2024
Hello thanks for the wonderful package. Can you please add support for this https://www.gsea-msigdb.org/gsea/msigdb/ Especially for getting gene sets Open

enhancement

Difficulty 4/5 3-5 days Newbie friendliness 30/100

scverse/gget#139 · Opened Jun 13, 2024
Module to download MitoCarta3 database Open

enhancement

Difficulty 3/5 1-2 days Newbie friendliness 35/100

scverse/gget#118 · Opened Jan 9, 2024
Add module for reactome Open

enhancement

Difficulty 5/5 Over a week Newbie friendliness 20/100

scverse/gget#114 · Opened Nov 29, 2023
GENCODE GTFs+FASTAs Open

enhancement

Difficulty 4/5 3-5 days Newbie friendliness 35/100

scverse/gget#73 · 1 reaction · Opened Apr 7, 2023
gget blast can not restrict by taxonomy Open

enhancement

Difficulty 4/5 3-5 days Newbie friendliness 35/100

scverse/gget#71 · 2 reactions · Opened Apr 5, 2023
Ability to match parameters of BLAST as per the web app Open

enhancement

Difficulty 4/5 3-5 days Newbie friendliness 28/100

scverse/gget#58 · 2 comments · Opened Jan 21, 2023
[gget_alphafold] - Feature Request - Add an option to submit a MSA instead of a protein sequence Open

enhancement

Difficulty 5/5 Over a week Newbie friendliness 25/100

scverse/gget#52 · 1 comment · Opened Jan 9, 2023
Request databases to be added to gget Open

enhancement

Difficulty 5/5 Over a week Newbie friendliness 25/100

scverse/gget#19 · 3 comments · Opened Jun 13, 2022
Add feature to fetch UCSC IDs Open

enhancement

Difficulty 4/5 3-5 days Newbie friendliness 42/100

scverse/gget#18 · Opened Jun 10, 2022

scverse/gget

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