tangermeme Genomic Model Analysis
jmschrei/tangermeme
Routes agents to the right tangermeme reference for analyzing trained genomic deep learning models, from attributions and motif experiments to variant effects and design.
Predict genome-wide functional tracks (RNA-seq, CAGE, DNase, ChIP) from DNA sequence with Borzoi.
Install Borzoi
$ npx skills add JimLiu/science-skills --skill borzoi -a claude-codeProject install by default; add -g for ~/.claude/skills/.
$ gh skill install JimLiu/science-skills borzoi --agent claude-codeProject scope by default; add --scope user for a personal install. Needs GitHub CLI 2.90.0 or later (public preview).
$ git clone --depth 1 https://github.com/JimLiu/science-skills.git skills-src && mkdir -p .claude/skills && cp -r skills-src/skills/borzoi .claude/skills/borzoi && rm -rf skills-srcUse ~/.claude/skills/ instead of .claude/skills for a personal install. The folder must contain SKILL.md.
Claude Code skills documentation · loads skills from .claude/skills/
Install the "borzoi" agent skill from https://github.com/JimLiu/science-skills/tree/main/skills/borzoi into .claude/skills/borzoi/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "borzoi", then confirm the skill loads.Claude Code copies the folder itself, the same result as the manual copy. Check what it changed before you commit it.
$skill-installer install https://github.com/JimLiu/science-skills/tree/main/skills/borzoiType this inside Codex. $skill-installer <name> installs a curated skill from openai/skills. The installer writes to $CODEX_HOME/skills (default ~/.codex/skills). Restart Codex if the skill does not show up.
$ npx skills add JimLiu/science-skills --skill borzoi -a codexProject install goes to .agents/skills/; add -g for ~/.codex/skills/.
$ gh skill install JimLiu/science-skills borzoi --agent codexProject scope by default (.agents/skills/); add --scope user for a personal install.
$ git clone --depth 1 https://github.com/JimLiu/science-skills.git skills-src && mkdir -p .agents/skills && cp -r skills-src/skills/borzoi .agents/skills/borzoi && rm -rf skills-srcUse ~/.agents/skills/ instead of .agents/skills for a personal install.
Codex skills documentation · loads skills from .agents/skills/
Install the "borzoi" agent skill from https://github.com/JimLiu/science-skills/tree/main/skills/borzoi into .agents/skills/borzoi/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "borzoi", then confirm the skill loads.Codex copies the folder itself, the same result as the manual copy. Check what it changed before you commit it.
$ npx skills add JimLiu/science-skills --skill borzoi -a cursorProject install goes to .agents/skills/; add -g for ~/.cursor/skills/.
$ gh skill install JimLiu/science-skills borzoi --agent cursorProject scope by default (.agents/skills/); add --scope user for a personal install.
$ git clone --depth 1 https://github.com/JimLiu/science-skills.git skills-src && mkdir -p .cursor/skills && cp -r skills-src/skills/borzoi .cursor/skills/borzoi && rm -rf skills-srcUse ~/.cursor/skills/ instead of .cursor/skills for a personal install.
Cursor skills documentation · loads skills from .cursor/skills/, .agents/skills/, .claude/skills/, .codex/skills/
Install the "borzoi" agent skill from https://github.com/JimLiu/science-skills/tree/main/skills/borzoi into .cursor/skills/borzoi/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "borzoi", then confirm the skill loads.Cursor copies the folder itself, the same result as the manual copy. Check what it changed before you commit it.
$ gemini skills install https://github.com/JimLiu/science-skills.git --path skills/borzoi--scope user (default) or --scope workspace; --path is the subfolder of the repo that holds the skill; --consent skips the security confirmation prompt.
$ npx skills add JimLiu/science-skills --skill borzoi -a gemini-cliProject install goes to .agents/skills/; add -g for ~/.gemini/skills/.
$ gh skill install JimLiu/science-skills borzoi --agent gemini-cliProject scope by default (.agents/skills/); add --scope user for a personal install.
$ git clone --depth 1 https://github.com/JimLiu/science-skills.git skills-src && mkdir -p .gemini/skills && cp -r skills-src/skills/borzoi .gemini/skills/borzoi && rm -rf skills-srcUse ~/.gemini/skills/ instead of .gemini/skills for a personal install, then run /skills reload.
Gemini CLI skills documentation · loads skills from .gemini/skills/, .agents/skills/
Install the "borzoi" agent skill from https://github.com/JimLiu/science-skills/tree/main/skills/borzoi into .gemini/skills/borzoi/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "borzoi", then confirm the skill loads.Gemini CLI copies the folder itself, the same result as the manual copy. Check what it changed before you commit it.
$ gh skill install JimLiu/science-skills borzoiInstalls for Copilot at project scope by default; add --scope user for a personal install. Preview a skill first with gh skill preview. Needs GitHub CLI 2.90.0 or later (public preview).
$ npx skills add JimLiu/science-skills --skill borzoi -a github-copilotProject install goes to .agents/skills/; add -g for ~/.copilot/skills/.
$ git clone --depth 1 https://github.com/JimLiu/science-skills.git skills-src && mkdir -p .github/skills && cp -r skills-src/skills/borzoi .github/skills/borzoi && rm -rf skills-srcUse ~/.copilot/skills/ instead of .github/skills for a personal install. Commit .github/skills so cloud agent and code review can use it.
GitHub Copilot skills documentation · loads skills from .github/skills/, .claude/skills/, .agents/skills/
Install the "borzoi" agent skill from https://github.com/JimLiu/science-skills/tree/main/skills/borzoi into .github/skills/borzoi/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "borzoi", then confirm the skill loads.GitHub Copilot copies the folder itself, the same result as the manual copy. Check what it changed before you commit it.
$ npx skills add JimLiu/science-skills --skill borzoi -a opencodeOpenCode documents no install command of its own. Project install goes to .agents/skills/; add -g for ~/.config/opencode/skills/.
$ gh skill install JimLiu/science-skills borzoi --agent opencodeProject scope by default (.agents/skills/); add --scope user for a personal install.
$ git clone --depth 1 https://github.com/JimLiu/science-skills.git skills-src && mkdir -p .opencode/skills && cp -r skills-src/skills/borzoi .opencode/skills/borzoi && rm -rf skills-srcUse ~/.config/opencode/skills/ instead of .opencode/skills for a personal install.
OpenCode skills documentation · loads skills from .opencode/skills/, .claude/skills/, .agents/skills/
Install the "borzoi" agent skill from https://github.com/JimLiu/science-skills/tree/main/skills/borzoi into .opencode/skills/borzoi/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "borzoi", then confirm the skill loads.OpenCode copies the folder itself, the same result as the manual copy. Check what it changed before you commit it.
Facts
- Skill name
borzoi- GitHub stars
- 227
- Used in
- 4 other repos
- Token cost
- ~973 tokens
- SKILL.md length
- 224 words
- Files
- 1
- Skills in repo
- 27
- Repo updated
- First seen
- Licence
- Apache-2.0
At a glance
Predict genome-wide functional tracks (RNA-seq, CAGE, DNase, ChIP) from DNA sequence with Borzoi.
- Scoring the regulatory effect of a variant on expression/accessibility
- SKILL.md covers Prerequisites, How to run, Output format and Remote compute, plus 1 more section
- Instructions only: no scripts, shell commands, URLs or credentials in SKILL.md
- Generating predicted coverage tracks for a locus
What it does
Borzoi is an agent skill from JimLiu/science-skills. Predict genome-wide functional tracks (RNA-seq, CAGE, DNase, ChIP) from DNA sequence with Borzoi. Use this skill when: (1) Scoring the regulatory effect of a variant on expression/accessibility, (2) Generating predicted coverage tracks for a locus, (3) Prioritising non-coding variants by predicted track delta.
Its SKILL.md is about 970 tokens, which your agent loads only when the skill is triggered. It is a single SKILL.md file with no bundled scripts.
It sits in Research & Science, covering Bioinformatics. It works with PyTorch. The licence is Apache-2.0.
When your agent uses it
- Scoring the regulatory effect of a variant on expression/accessibility
- Generating predicted coverage tracks for a locus
- Prioritising non-coding variants by predicted track delta
Example prompts
- “/borzoi”
Requirements
- Python 3
What it can do on your machine
Read from SKILL.md and the folder at commit fb309c3. It shows what the files ask for, not the result of running them.
Tool permissions
Pre-approves nothing: there is no allowed-tools line, so your agent's usual permission prompts apply.
From allowed-tools in the SKILL.md frontmatter.
Runs code
No scripts in the folder and no shell commands in SKILL.md (its code samples are python).
From the folder's file list and the shell code blocks in SKILL.md.
Network
No URLs in SKILL.md.
From URLs in SKILL.md, links to its own repository left out.
Credentials
Names no API keys, tokens, secrets or passwords.
From names ending in _API_KEY, _TOKEN, _SECRET, _KEY or _PASSWORD in SKILL.md.
Context cost
Borzoi loads about 973 tokens when it runs. Until then it costs about 80 tokens; SKILL.md has 224 words of instructions outside code blocks.
Estimates: characters ÷ 4, the usual rule of thumb; real counts depend on the model's tokenizer. Scripts and assets cost tokens only if the agent reads them.
Safety
Auto-check passed
The automated check found no risky patterns in SKILL.md.
Automated static check — not a guarantee. Review scripts before installing. It scans the text of SKILL.md for risky patterns (piping downloads into a shell, reading credential files, hidden Unicode, destructive commands); files beside SKILL.md are not scanned.
SKILL.md
The full file from JimLiu/science-skills at commit fb309c3, republished under its Apache-2.0 licence (© JimLiu). 224 words, ~973 tokens.
Download SKILL.mdSave it as
.claude/skills/borzoi/SKILL.md (or your agent's skills folder).- name
- borzoi
- description
- Predict genome-wide functional tracks (RNA-seq, CAGE, DNase, ChIP) from DNA sequence with Borzoi. Use this skill when: (1) Scoring the regulatory effect of a variant on expression/accessibility, (2) Generating predicted coverage tracks for a locus, (3) Prioritising non-coding variants by predicted track delta.
- license
- Apache-2.0
- category
- biomodels
- requirements
- gpu
Borzoi — DNA → Functional Track Prediction
Prerequisites
| Requirement | Minimum | Recommended |
|---|---|---|
| Python | 3.10+ | 3.11 |
| CUDA | 12.1+ | 12.4+ |
| GPU VRAM | 16 GB | 24 GB+ |
How to run
from borzoi_pytorch import Borzoi
model = Borzoi.from_pretrained("johahi/borzoi-replicate-0").cuda().eval()
# input: (batch, 4, 524288) one-hot DNA → output: (batch, tracks, 6144) binsBorzoi consumes ~524 kb one-hot windows and emits binned predictions across
7,611 human tracks (the separate 2,608-track mouse head is off by default;
enable via enable_mouse_head=True and select with
forward(..., is_human=False)). For variant scoring, run ref/alt windows
centred on the variant and compare per-track output.
Output format
(B, T, L) tensor — T tracks × L 32-bp bins. Track metadata (assay,
biosample) is in borzoi_pytorch.pytorch_borzoi_model.TRACKS_DF (or model.tracks_df when using the AnnotatedBorzoi subclass) — the base Borzoi model has no targets attribute.
Remote compute
Needs ≥24 GB VRAM and either pre-cached HF weights or egress to
huggingface.co. Read compute_details({provider, mode:'read'}) for an
environment with borzoi-pytorch, then:
c = host.compute.create(provider)
job = c.submit_job(
intent="Borzoi track prediction for 1 locus — 1×GPU, ~2 min",
inputs=[{"src": "borzoi_run.py", "dst_filename": "borzoi_run.py"}],
command="python3 borzoi_run.py", # env selection is host-specific — see compute_details for your provider
outputs=["tracks.npz"],
timeout_seconds=1800,
)
print(job.job_id) # cell ends here — kernel never blocks on computeThen call the wait_for_notification brain-tool. When the
compute_done notification arrives, act on its payload:
save_artifacts(payload["featured_files"]) # paths under hpc/<job_id>/For the full result dict (output_files, remote_workdir, …), re-enter the
kernel: c.attach_job(job_id).result() then c.close(). See the
remote-compute-ssh / remote-compute-modal skill for the orchestration
details.
If the provider exposes a weight-cache mount, point HF_HOME at it inside
borzoi_run.py (path is in compute_details).
Troubleshooting
| Symptom | Cause | Fix |
|---|---|---|
module has no __version__ | Package exposes no attr | Use importlib.metadata.version("borzoi-pytorch") |
| Shape mismatch on input | Wrong window length | Pad/crop to 524288 bp (fixed; not exposed as a model attribute) |
Next: combine track deltas with evo2 likelihood deltas for a
two-axis variant prioritisation.
© JimLiu, Apache-2.0. Rendered from Markdown: HTML in the file is shown as text, images as links, and headings moved down two levels. Raw file
Files
Just SKILL.md in skills/borzoi of JimLiu/science-skills.
Open the folder on GitHubat commit fb309c3
Used in 4 other repositories
We found 4 copies of this SKILL.md (exact, near-identical or edited) in other folders, from 4 other GitHub owners. This page covers the copy in JimLiu/science-skills, which our catalogue first saw on October 7, 2026.
Compare with similar skills
Borzoi next to the 5 skills that share the most tags, products or categories with it. Stars are the repository's; “used in” counts other GitHub owners with a copy.
| Skill | Stars | Used in | Tokens | Auto-check | Licence | Repo updated |
|---|---|---|---|---|---|---|
| Borzoi this skillJimLiu/science-skills | 227 | 4 repos | ~973 | Automated safety check: Pass | Apache-2.0 | |
| tangermeme Genomic Model Analysisjmschrei/tangermeme | 316 | — | ~1.6k | Automated safety check: Pass | MIT | |
| Cellxgene Censusdavila7/claude-code-templates | 32k | 11 repos | ~3.8k | Automated safety check: Pass | MIT | |
| Pixi Environment Builderxuzhougeng/wisp-science | 1k | — | ~3.7k | Automated safety check: Pass | AGPL-3.0 | |
| Alphagenome Predictionsgenomicsxai/alphagenome-pytorch | 162 | — | ~868 | Automated safety check: Pass | Apache-2.0 | |
| Alphagenome Single Variant Analysisgoogle-deepmind/science-skills | 3.2k | 2 repos | ~3k | Automated safety check: Notes | Apache-2.0 |
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Analyzes genetic variant effects on gene expression (RNA-seq), chromatin accessibility (DNASE), histone marks (ChIP), and transcription factors using the AlphaGenome API.
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Related
Works with
Categories
Questions about Borzoi
What does Borzoi do?
Predict genome-wide functional tracks (RNA-seq, CAGE, DNase, ChIP) from DNA sequence with Borzoi. Borzoi is an agent skill from JimLiu/science-skills. Predict genome-wide functional tracks (RNA-seq, CAGE, DNase, ChIP) from DNA sequence with Borzoi.
When should I use Borzoi?
Borzoi fits situations like: scoring the regulatory effect of a variant on expression/accessibility; generating predicted coverage tracks for a locus; prioritising non-coding variants by predicted track delta.
How do I install Borzoi in Claude Code?
Run `npx skills add JimLiu/science-skills --skill borzoi -a claude-code`. Or copy the skill folder (skills/borzoi in JimLiu/science-skills) into .claude/skills/borzoi in your project. Claude Code loads it when a task matches its description.
How do I install Borzoi in Codex?
Run `npx skills add JimLiu/science-skills --skill borzoi -a codex`. Or copy the skill folder (skills/borzoi in JimLiu/science-skills) into .agents/skills/borzoi in your project. Codex loads it when a task matches its description.
Can I use Borzoi in Cursor, Gemini CLI or GitHub Copilot?
Cursor, Gemini CLI, GitHub Copilot and OpenCode also load SKILL.md folders. With the skills CLI, run `npx skills add JimLiu/science-skills --skill borzoi -a cursor` (or -a gemini-cli, github-copilot or opencode for the others). To copy it by hand, put the folder in .cursor/skills/borzoi, .gemini/skills/borzoi, .github/skills/borzoi and .opencode/skills/borzoi in your project.
What does Borzoi need to run?
SKILL.md names no scripts, command-line tools or credentials: Borzoi is instructions for the agent only. Our summary lists: Python 3.
Does Borzoi access the network?
SKILL.md contains no URLs. Any network use would come from the scripts or tools the agent runs. This is read from the text; nothing was executed.
Is Borzoi safe to install?
Our automated static check of SKILL.md found no risky patterns, such as piping downloads into a shell, reading credential files or hidden Unicode. It is not a guarantee. Review the folder before installing.
What licence does Borzoi use?
Borzoi is published under the Apache-2.0 licence (declared in SKILL.md). It allows redistribution, so the full SKILL.md is shown on this page.
How many tokens does Borzoi use?
About 973 tokens (SKILL.md is roughly 3.9k characters). Agents keep only the skill's name and description in context until a task matches; then they load SKILL.md in full.
What are the alternatives to Borzoi?
Skills that share tags, products or a category with Borzoi: tangermeme Genomic Model Analysis (jmschrei/tangermeme, 316 stars), Cellxgene Census (davila7/claude-code-templates, 32k stars), Pixi Environment Builder (xuzhougeng/wisp-science, 1k stars) and Alphagenome Predictions (genomicsxai/alphagenome-pytorch, 162 stars). The comparison table on this page puts their stars, adoption, token cost, safety result and licence side by side.
Who maintains Borzoi?
JimLiu (a GitHub user) maintains it in JimLiu/science-skills, which has 227 GitHub stars. The repository holds 27 skills in this directory. The repository was last updated on July 1, 2026.
Source: JimLiu/science-skills on GitHub. Facts on this page come from the repository at the commit we read; the author's words are quoted as theirs.