Knowledge Work Plugins is an open-source collection of Claude extensions organized around roles such as productivity, sales, and customer support. Each plugin combines role-specific guidance, connectors, commands, and sub-agents so knowledge workers can use Claude with their team’s tools and processes. The catalogue entries are examples of, or workflows from, this plugin collection.
Getting it into your agent
One page per mod, every tool's command on it. A separate URL per tool would split the same page into five that compete with each other.
npx skills add anthropics/knowledge-work-plugins --skill scvi-toolsgit clone --depth 1 https://github.com/anthropics/knowledge-work-pluginsWrote this? Show the measurements
A badge with what this costs and how it scanned, read live from this page, so it follows the numbers instead of freezing them. Markdown for a README, HTML for a documentation site or a project page.
[](https://agentmods.dev/skills/anthropics/knowledge-work-plugins/scvi-tools)<a href="https://agentmods.dev/skills/anthropics/knowledge-work-plugins/scvi-tools"><img src="https://agentmods.dev/badge/skills/anthropics/knowledge-work-plugins/scvi-tools/github.svg" alt="Measured on agentmods" height="20"></a>Or the 80×15 button, for a site that already has a row of RSS and ATOM ones. Only the verdict fits; the numbers stay here.
<a href="https://agentmods.dev/skills/anthropics/knowledge-work-plugins/scvi-tools"><img src="https://agentmods.dev/badge/skills/anthropics/knowledge-work-plugins/scvi-tools.svg" alt="Reviewed on agentmods" width="80" height="20"></a>- Socket pass
- Snyk pass
- NVIDIA SkillSpector pass
What it costs to keep this loaded
Counted locally with the o200k_base tokenizer, which is exact for GPT models; Claude uses its own tokenizer and its counts differ. Treat this as one consistent yardstick across the catalogue rather than a bill. Prices are per million input tokens.
| Model | Per session | Once invoked |
|---|---|---|
| Fable 5.1 | $0.00193 | $0.01867 |
| Opus 5.5 | $0.00077 | $0.00747 |
| Sonnet 5.5 | $0.00039 | $0.00373 |
| Haiku 4.5 | $0.00019 | $0.00187 |
Grade A, and why
scvi-tools scanned grade A with 0 findings against 26 rules in 11 categories — prompt injection, anti-refusal, data exfiltration, privilege escalation, supply chain, agent snooping, system-prompt leakage, SSRF and excessive agency — measured 1mo ago.
A static scan of the body, not an audit. Every finding is printed with the line that produced it so you can judge whether it matters here. A mod is markdown that instructs an agent; that is exactly why what it instructs is worth reading.
Nothing flagged
None of the 26 patterns this scan looks for appear in this file: no shell pipes, no recursive deletes, no credential paths, no hidden text, no instruction-override or anti-refusal phrasing, no agent-config snooping. That is not a guarantee, it is the absence of the things that are checkable.
Copies of this mod
4 near-identical copies found in the catalogue:
- scvi-tools — 100% identical, 0 lines differ
- scvi-tools — 100% identical, 0 lines differ
- scvi-tools — 100% identical, 0 lines differ
- scvi-tools — 100% identical, 11 lines differ
How it starts
The opening of the file, as written. The whole thing — 156 lines — stays where its author put it; the contents beside it link to each section on GitHub.
scvi-tools Deep Learning Skill
This skill provides guidance for deep learning-based single-cell analysis using scvi-tools, the leading framework for probabilistic models in single-cell genomics.
How to Use This Skill
- Identify the appropriate workflow from the model/workflow tables below
- Read the corresponding reference file for detailed steps and code
- Use scripts in
scripts/to avoid rewriting common code - For installation or GPU issues, consult
references/environment_setup.md - For debugging, consult
references/troubleshooting.md
When to Use This Skill
- When scvi-tools, scVI, scANVI, or related models are mentioned
- When deep learning-based batch correction or integration is needed
- When working with multi-modal data (CITE-seq, multiome)
- When reference mapping or label transfer is required
- When analyzing ATAC-seq or spatial transcriptomics data
- When learning latent representations of single-cell data
Model Selection Guide
| Data Type | Model | Primary Use Case |
|---|---|---|
| scRNA-seq | scVI | Unsupervised integration, DE, imputation |
| scRNA-seq + labels | scANVI | Label transfer, semi-supervised integration |
| CITE-seq (RNA+protein) | totalVI | Multi-modal integration, protein denoising |
| scATAC-seq | PeakVI | Chromatin accessibility analysis |
| Multiome (RNA+ATAC) | MultiVI | Joint modality analysis |
| Spatial + scRNA reference | DestVI | Cell type deconvolution |
| RNA velocity | veloVI | Transcriptional dynamics |
| Cross-technology | sysVI | System-level batch correction |
Workflow Reference Files
| Workflow | Reference File | Description |
|---|---|---|
| Environment Setup | references/environment_setup.md |
Installation, GPU, version info |
| Data Preparation | references/data_preparation.md |
Formatting data for any model |
| scRNA Integration | references/scrna_integration.md |
scVI/scANVI batch correction |
| ATAC-seq Analysis | references/atac_peakvi.md |
PeakVI for accessibility |
| CITE-seq Analysis | references/citeseq_totalvi.md |
totalVI for protein+RNA |
| Multiome Analysis | references/multiome_multivi.md |
MultiVI for RNA+ATAC |
| Spatial Deconvolution | references/spatial_deconvolution.md |
DestVI spatial analysis |
| Label Transfer | references/label_transfer.md |
scANVI reference mapping |
| scArches Mapping | references/scarches_mapping.md |
Query-to-reference mapping |
| Batch Correction | references/batch_correction_sysvi.md |
Advanced batch methods |
| RNA Velocity | references/rna_velocity_velovi.md |
veloVI dynamics |
| Troubleshooting | references/troubleshooting.md |
Common issues and solutions |
What ships with it
21 files beside SKILL.md in the same directory: the scripts, references and assets a skill reads on demand. Not counted in the per-session cost; read them before you install if any of them is executable.
- LICENSE.txt 10 KB
- references/atac_peakvi.md 9.3 KB
- references/batch_correction_sysvi.md 10 KB
- references/citeseq_totalvi.md 10 KB
- references/data_preparation.md 6.2 KB
- references/environment_setup.md 6.3 KB
- references/label_transfer.md 10 KB
- references/multiome_multivi.md 8.9 KB
- references/rna_velocity_velovi.md 8.6 KB
- references/scarches_mapping.md 11 KB
- references/scrna_integration.md 9.6 KB
- references/spatial_deconvolution.md 11 KB
- references/troubleshooting.md 11 KB
- scripts/cluster_embed.py 6.3 KB runs code
- scripts/differential_expression.py 6.7 KB runs code
- scripts/integrate_datasets.py 6.9 KB runs code
- scripts/model_utils.py 17 KB runs code
- scripts/prepare_data.py 5.1 KB runs code
- scripts/train_model.py 11 KB runs code
- scripts/transfer_labels.py 7.2 KB runs code
- scripts/validate_adata.py 12 KB runs code
What this file has done since we first saw it
Hashed on every crawl. A supply-chain change to an agent config is a question of when, not whether, so the history is kept rather than the latest state alone.
- 1mo ago First seen · 156 lines · 193 tokens per session scan A 03a69b32b77d
scvi-tools is a skill published in the GitHub repository anthropics/knowledge-work-plugins (29,887 stars, last pushed yesterday), licensed Apache-2.0. It adds 193 tokens to every session and 1,867 once invoked, about $0.0008 per session on Opus 5.5. A static security scan graded it A with 0 findings. No closer match exists in the catalogue, so it is treated as the original; first seen 2026-08-30.
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