Individual skill
scvi-tools
Fits probabilistic models for single-cell omics, including scVI batch integration, scANVI annotation, totalVI CITE-seq, MultiVI RNA/ATAC integration, and posterior differential expression. Use for generative modeling, reference mapping, multimodal analysis, or model-based uncertainty; use scanpy for standard preprocessing and exploratory analysis.
skills/scvi-tools/SKILL.md
Source commit 2d2065fb4520fa3f3f2bcf61cff26ec8b7eba4b5
What was checked
- Matches the observed repository HEAD
- Yes
- Scanner rules are current
- No
- Repository scan complete
- No
- Skill scan complete
- No
- Observed behavior
- Not checked yet
- Last checked
- Nov 10, 2026
These are observations at the recorded commit, not a guarantee of safety. Review the source before running it.
Install this skill
Choose an agent in your Stack or copy a command below. Commands fetch the pinned commit and copy only this skill directory. Existing destinations are refused. Copying a command does not install anything.
An install command is unavailable: current rules, complete repository and skill scans, an eligible behavior level and a permitted license are required.
Repository context
- Repository stars (not skill ratings)
- 56,903
- Repository last updated
- Nov 9, 2026
- License
- MIT
Observed agent integration: No specific integration evidence. Standard SKILL.md installation does not imply verified compatibility.
- ai-scientist Repository topic
- bioinformatics Repository topic
- chemoinformatics Repository topic
- claude Repository topic
- claude-skills Repository topic
- claudecode Repository topic
- clinical-research Repository topic
- computational-biology Repository topic
- data-analysis Repository topic
- drug-discovery Repository topic
- engineering Derived category
Files and excerpt
File metadata and permitted, redacted excerpts come from the recorded scan. Source links are pinned to that commit.
Browse files
SKILL.mdcore · 10,233 bytesSKILL.mdcore · 10,233 bytesSKILL.mdcore · 10,233 bytesSKILL.mdcore · 10,233 bytesSKILL.mdcore · 10,233 bytesSKILL.mdcore · 10,233 bytesSKILL.mdcore · 10,233 bytesreferences/differential-expression.mddoc · 7,095 bytesreferences/models-atac-seq.mddoc · 5,741 bytesreferences/models-multimodal.mddoc · 8,476 bytesreferences/models-scrna-seq.mddoc · 7,931 bytesreferences/models-spatial.mddoc · 9,087 bytesreferences/models-specialized.mddoc · 6,509 bytesreferences/theoretical-foundations.mddoc · 5,240 bytesreferences/workflows.mddoc · 9,300 bytes
Read excerpt
# scvi-tools
Targets **scvi-tools 1.5.1**, released September 10, 2026. APIs below were checked
against the tagged source and official documentation. The examples are illustrative:
the repository tests exercise short CPU synthetic fits for SCVI, SCANVI, TOTALVI,
MULTIVI, METHYLVI, PEAKVI and POISSONVI, plus count-preserving preprocessing,
DE output contracts, save/load and minification. The tested stack is Python 3.13,
Scanpy 1.12.4, AnnData 0.13.4, MuData 0.4.1, PyTorch 2.14.1 and Lightning 2.6.6.
Long training, hardware-specific paths and other specialized workflows remain
illustrative; these checks do not establish convergence or biological validity.
## Choose the model and its input contract
| Task | Class | Required input |