perturbseq-hypotheses SKILL.md skillA
perturbseq-hypotheses from engreitzlab/perturbnmf is an agent skill: a SKILL.md folder an AI agent loads when a task calls for it.
mdr add engreitzlab/perturbnmf/perturbseq-hypotheses@git:20261019.294698dPins git:20261019.294698d in mdr.lock. Pin the fingerprint instead.
- Audit grade
- A, 17 of 17 checks passed
- Kind
- SKILL.md skill
- Repository
- engreitzlab/perturbnmf
- Path
src/Stage3_Interpretation/C_Annotation/4.Hypothesis/perturbseq-hypotheses/SKILL.md- Versions recorded
- 1
- Latest version
- git:20261019.294698d, committed Oct 19, 2026
- Size
- 15,560 bytes
- Repository stars
- 10
- License
- MIT
Turn a finished Perturb-seq / PerturbNMF screen (cNMF programs, per-perturbation effect tables, NTC null, regulator correlation matrix, enrichment tables) into a short, curated report of the top N (default 10) researched biological hypotheses. Each is a mechanistic claim that survived falsification tests on the data, a literature check and at least one round of revision, and each comes with plots, integrated literature and a concrete experiment. It runs as an iterative multi-agent loop…
Collected from public GitHub. Every version is saved exactly as it was and never changes. Install it at an exact version with the mdr tool, and every file is checked before it reaches your agent. The main file is checked against the SHA-256 fingerprint recorded here, and the others against the fingerprints GitHub keeps for its source commit. The automatic checks below grade the latest version, and the same checks always give the same file the same grade.
What the file says
# Perturb-seq hypotheses Produce the **top N hypotheses a screen supports**, where each one has been proposed, tested against the data, checked against the literature, and revised or killed until what is left is worth an experiment. The deliverable is a list of hypotheses, not an account of how they were found. **Parameters** (in `study.yaml :: loop`, or given by the user): - `n_hypotheses`: default **10** - `effort`: `low` / `medium` / `high`, default `medium`. **Ask the user at the start, beside `study.yaml`.** It sets `candidates_per_hypothesis` unless that is given explicitly: | `effort` | `candidates_per_hypothesis` | Candidates for N = 10 | Use when | |---|---|---|---| | `low` | 2 | 20 | a quick first look | | `medium` | 3 | 30 | the default | | `high` | 9 | 90 | a screen worth a full run. Roughly 3× the agents and time of `medium` | About one candidate in ten survives the loop, so `medium` often ships fewer than N. Say so when asking. - `max_rounds`: default 3 - `human_steer_after_round_1`: default false > **Teaching examples in this skill must never name findings from a screen it will be run on.** …
Read the whole file at its exact version.
How to install
mdr add engreitzlab/perturbnmf/perturbseq-hypotheses@sha256:dd70da7e8cc6e097The line at the top of this page pins the label git:20261019.294698d, which is what most people want. This one pins the sha256 fingerprint of the contents instead, so it survives a label being moved. Either way the exact version is written to mdr.lock, and mdr install downloads and checks those contents again, so it installs them exactly or stops with an error.
[](https://markdownregistry.com/a/art_xr53jwswcf5kq5zm)
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Versions
The registry has recorded 1 version of this file, committed on Oct 19, 2026.
Audit of the latest version
- pass: Frontmatter block present
- pass: Frontmatter declares a name
- pass: Frontmatter declares a description
- pass: Size between 200 bytes and 200 KB (15560 bytes)
- pass: No zero-width or bidi control characters
- pass: No instruction hidden inside an HTML comment
- pass: No link to an exfiltration or paste host
- pass: No credential-shaped string
- pass: No instruction to send local credentials anywhere
- pass: No text hidden with inline styles
- pass: No prompt-injection phrasing
- pass: No curl or wget piped into a shell
- pass: No recursive delete of root, home or parent
- pass: No instruction to read or print local credentials
- pass: No base64 blob over 200 characters
- pass: No link to a raw IP address
- pass: No script tag
Source
engreitzlab/perturbnmf · 10 stars · license MIT · pushed 2026-10-20 · branch main
API
GET https://markdownregistry.com/api/v1/artifacts/art_xr53jwswcf5kq5zm GET https://markdownregistry.com/api/v1/resolve?ref=engreitzlab/perturbnmf/perturbseq-hypotheses GET https://markdownregistry.com/api/v1/blob/dd70da7e8cc6e0977a4aa9c8dbe45028a583e2d10062807f7296c21237347617
Your AI assistant does the legwork. You hear about the deals worth your word. Hand yours the standing instructions at modelranch.com and it joins the network that reads files like this one.
Guides: the SKILL.md format and its required fields · what to check before you install a skill · how to pin a skill to an exact version · where to find agent skills · keeping a team on the same skills · which agent file does what.