biocore/redbiom

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Sample search by metadata and features

Stars: 49
Forks: 18
Open beginner issues: 0
Indexed issues: 25

Dominant language: Python
License: No license data
Last GitHub push: Aug 31, 2023
Latest indexed: Sep 14, 2026
Contributing guide: No contributing guide
Code of conduct: No code of conduct
Beginner labels: No beginner labels indexed
PR merge metrics: No merged PRs in 30d

Open All

25 open issues indexed

Store a tree, and provide means to subset Open

server-side-support

biocore/redbiom#6 · 1 comment · 0 reactions · 0 assignees · Indexed Sep 14, 2026
Support metadata that contains "/" characters Open

server-side-support

biocore/redbiom#9 · 1 comment · 0 reactions · 0 assignees · Indexed Sep 14, 2026
requests.buffered does not have the most intuitive of interfaces Open

server-side-support

biocore/redbiom#12 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 14, 2026
Set a context specific coherency flag on load of observation or sample data Open

server-side-support

biocore/redbiom#14 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 14, 2026
Support a default context Open

server-side-support

biocore/redbiom#23 · 1 comment · 0 reactions · 0 assignees · Indexed Sep 14, 2026
It should be possible to summarize metadata within a context Open

biocore/redbiom#24 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 14, 2026
`redbiom summarize metadata` is not handling from stdin Open

biocore/redbiom#26 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 14, 2026
`redbiom search observations` should search all contexts if one is not provided Open

server-side-support

biocore/redbiom#27 · 1 comment · 0 reactions · 0 assignees · Indexed Sep 14, 2026
substring matching via SCAN Open

server-side-support

biocore/redbiom#28 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 14, 2026
Let "redbiom fetch sample-metadata" print to stdout Open

biocore/redbiom#39 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 14, 2026
Discrepancy between metadata search and stored metadata Open

server-side-support

biocore/redbiom#40 · 1 comment · 0 reactions · 0 assignees · Indexed Sep 14, 2026
It should be possible to easily discover the metadata categories for a set of samples Open

biocore/redbiom#42 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 14, 2026
On fetch, use HMGET Open

biocore/redbiom#45 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 14, 2026
Remove whole contexts Open

server-side-support

biocore/redbiom#51 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 14, 2026
Uniquify Open

biocore/redbiom#60 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 14, 2026
parallel support via joblib Open

biocore/redbiom#61 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 14, 2026
It should be possible to guess a context Open

biocore/redbiom#63 · 1 comment · 0 reactions · 0 assignees · Indexed Sep 14, 2026
Contexts should optionally store machine readable processing information Open

biocore/redbiom#64 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 14, 2026
It would be nice to get the list of features in samples Open

biocore/redbiom#65 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 14, 2026
Allow select samples from metadata to support cross-context queries Open

biocore/redbiom#71 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 14, 2026
Fetch qiita-study --md5 should be is_flag Open

biocore/redbiom#123 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 14, 2026
Discrepancy between metadata search results & piped fetch results Open

biocore/redbiom#125 · 4 comments · 0 reactions · 0 assignees · Indexed Sep 14, 2026
Verify redbiom test suite works with Redis 7 Open

biocore/redbiom#127 · 4 comments · 0 reactions · 1 assignee · Indexed Sep 14, 2026
Connection to qiita.ucsd.edu timed out. Open

biocore/redbiom#130 · 17 comments · 0 reactions · 0 assignees · Indexed Sep 14, 2026
Resource punkt_tab not found. Open

biocore/redbiom#131 · 2 comments · 0 reactions · 0 assignees · Indexed Sep 14, 2026

biocore/redbiom

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