Skills

scvelo

scvelo is a skill in K-Dense-AI/scientific-agent-skills, last changed 1 Oct 2026. It can run shell commands, reach the network, name web addresses and bundle scripts — read the findings before installing. Our pattern check flagged nothing at commit 5f2bc03 on 26 Oct 2026.

Pattern check: nothing flagged · commit 5f2bc03 · 26 Oct 2026

Install
From the author
Performs RNA velocity analysis with scVelo from spliced and unspliced single-cell RNA counts. Fits deterministic or dynamical models, examines gene phase portraits, builds velocity graphs, estimates relative latent time, and ranks velocity-associated genes. Use for directional trajectory hypotheses and kinetic-model diagnostics alongside Scanpy; velocity alone does not establish cell fate or causal drivers.
Licence
BSD 3-Clause
Repo stars
54.8k
Folder last changed
1 Oct 2026 (opens in a new tab)
Publisher
K-Dense-AI
Files
3 files
Checked
5f2bc03 (opens in a new tab) · 26 Oct 2026

Install

Each tab says whether it installs commit 5f2bc03, the one we checked, or the latest version.

No tab for your agent? Use Any agent for OpenCode, Goose, Windsurf (Devin Desktop), Zed, Roo Code, Factory Droid, Junie, Amp and Antigravity, and Claude Code for Cline. Kiro needs the folder copied by hand.

Pinned to commit 5f2bc03, the one we checked.

From your project's root folder:

tmp="$(mktemp -d)" &&
  git clone -q --depth 1 --filter=blob:none --no-checkout https://github.com/K-Dense-AI/scientific-agent-skills.git "$tmp" &&
  git -C "$tmp" fetch -q --depth 1 origin 5f2bc0341354fd5590aef76a533ada1e1e5b4e62 &&
  git -C "$tmp" sparse-checkout set -- skills/scvelo &&
  git -C "$tmp" checkout -q 5f2bc0341354fd5590aef76a533ada1e1e5b4e62 &&
  mkdir -p .claude/skills &&
  mkdir .claude/skills/scvelo &&
  cp -R "$tmp"/skills/scvelo/. .claude/skills/scvelo/ &&
  rm -rf "$tmp"

If Claude Code was already running and this created the skills folder, run /reload-skills.

Claude Code docs (opens in a new tab)

What it can touch

From the files and frontmatter at commit 5f2bc03. This is how much a skill can do, not whether it is risky.

What it can touch: Shell, network or credentials

  • Runs shell commands

    Its instructions or files give the agent commands to run on your computer.

  • Reaches the network

    It sends or fetches data over the internet, for example with curl, an HTTP library or a package install.

  • Names web addresses

    It mentions outside web addresses the agent may visit. We list them but don't follow them.

  • Bundles scripts

    The folder holds code files the agent may run.

Pattern check

Pattern check: nothing flagged · commit 5f2bc03 · 26 Oct 2026

We checked every text file in this skill, at commit 5f2bc03 on 26 Oct 2026, against 45 published patterns such as download-and-run commands, hidden text and credential access. We don't run the skill, we don't read the web pages it points to, and we can't judge everything its instructions might lead an agent to do. In published tests, pattern checks like this one missed most malicious skills. Read the skill before you install it — especially anything it asks you to download or run.

How the check worksReport an incorrect finding

Outside links we did not follow

  • https://github.com/theislab/scvelo/tree/v0.3.4
  • https://scvelo.readthedocs.io/en/latest/api.html
  • https://scvelo.readthedocs.io/en/latest/perspectives/Perspectives.html
  • https://anndata.readthedocs.io/en/stable/generated/anndata.io.read_loom.html
  • https://doi.org/10.1038/s41587-020-0591-3
  • https://cellrank.readthedocs.io/en/stable/api/_autosummary/estimators/cellrank.estimators.GPCCA.html
  • https://github.com/theislab/scvelo/blob/v0.3.4/scvelo/preprocessing/utils.py
  • https://scvelo.readthedocs.io/en/latest/scvelo.tl.velocity_graph.html
  • https://scvelo.readthedocs.io/en/latest/scvelo.tl.recover_dynamics.html
  • https://github.com/theislab/scvelo/blob/v0.3.4/scvelo/tools/_em_model_core.py
Show 2 more
  • https://github.com/theislab/scvelo/blob/v0.3.4/scvelo/tools/velocity_confidence.py
  • https://scvelo.readthedocs.io/en/latest/scvelo.tl.rank_velocity_genes.html

Format check

Each agent reads SKILL.md a little differently. We check the file against each one's published rules; we don't run the skill in any agent.

  • Agent Skills specPasses

    The open format from agentskills.io, held to what the strictest agents enforce, so one folder loads everywhere.

    • Note

      Reference files over 100 lines with no table of contents at the top: references/velocity_models.md (185 lines). B5

      Fix: Add a short list of the sections at the top of each.

  • Claude CodePasses

    Claude Code reads its own extra fields, ignores unknown ones, and still loads a skill whose frontmatter is broken, without its fields.

    • Note

      Reference files over 100 lines with no table of contents at the top: references/velocity_models.md (185 lines). B5

      Fix: Add a short list of the sections at the top of each.

  • Claude apps & API uploadPasses

    Uploading to claude.ai or the Claude API, or packaging with Anthropic's script, accepts only the six spec fields and stops on anything else.

    • Note

      The description is 410 characters. The claude.ai Help Center says 200 at most, though Anthropic's API docs and validator allow 1,024. D4

      Fix: If the claude.ai upload refuses it, trim the description to 200 characters.

    • Note

      Reference files over 100 lines with no table of contents at the top: references/velocity_models.md (185 lines). B5

      Fix: Add a short list of the sections at the top of each.

  • OpenAI (Codex & API)Passes
  • VS Code & CopilotPasses

SKILL.md

Files

3 files

PathSize
SKILL.md (opens in a new tab)12.2 KB
references/velocity_models.md (opens in a new tab)9.2 KB
scripts/rna_velocity_workflow.py (opens in a new tab)12.9 KB

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