Arboreto
K-Dense-AI/scientific-agent-skills
Infers candidate gene regulatory networks from bulk or single-cell expression data using AertsLab Arboreto GRNBoost2 and GENIE3.
Fetch Evolutionary Conservation scores (phyloP, phastCons) and Transcription Factor Binding Sites (TFBS) from the UCSC Genome Browser.
$ npx skills add google-deepmind/science-skills --skill ucsc-conservation-and-tfbs -a claude-codeProject install by default; add -g for ~/.claude/skills/.
$ gh skill install google-deepmind/science-skills ucsc-conservation-and-tfbs --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/google-deepmind/science-skills.git skills-src && mkdir -p .claude/skills && cp -r skills-src/skills/ucsc_conservation_and_tfbs .claude/skills/ucsc-conservation-and-tfbs && 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 "ucsc-conservation-and-tfbs" agent skill from https://github.com/google-deepmind/science-skills/tree/main/skills/ucsc_conservation_and_tfbs into .claude/skills/ucsc-conservation-and-tfbs/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "ucsc-conservation-and-tfbs", 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/google-deepmind/science-skills/tree/main/skills/ucsc_conservation_and_tfbsType 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 google-deepmind/science-skills --skill ucsc-conservation-and-tfbs -a codexProject install goes to .agents/skills/; add -g for ~/.codex/skills/.
$ gh skill install google-deepmind/science-skills ucsc-conservation-and-tfbs --agent codexProject scope by default (.agents/skills/); add --scope user for a personal install.
$ git clone --depth 1 https://github.com/google-deepmind/science-skills.git skills-src && mkdir -p .agents/skills && cp -r skills-src/skills/ucsc_conservation_and_tfbs .agents/skills/ucsc-conservation-and-tfbs && rm -rf skills-srcUse ~/.agents/skills/ instead of .agents/skills for a personal install.
Codex skills documentation · loads skills from .agents/skills/
Install the "ucsc-conservation-and-tfbs" agent skill from https://github.com/google-deepmind/science-skills/tree/main/skills/ucsc_conservation_and_tfbs into .agents/skills/ucsc-conservation-and-tfbs/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "ucsc-conservation-and-tfbs", 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 google-deepmind/science-skills --skill ucsc-conservation-and-tfbs -a cursorProject install goes to .agents/skills/; add -g for ~/.cursor/skills/.
$ gh skill install google-deepmind/science-skills ucsc-conservation-and-tfbs --agent cursorProject scope by default (.agents/skills/); add --scope user for a personal install.
$ git clone --depth 1 https://github.com/google-deepmind/science-skills.git skills-src && mkdir -p .cursor/skills && cp -r skills-src/skills/ucsc_conservation_and_tfbs .cursor/skills/ucsc-conservation-and-tfbs && 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 "ucsc-conservation-and-tfbs" agent skill from https://github.com/google-deepmind/science-skills/tree/main/skills/ucsc_conservation_and_tfbs into .cursor/skills/ucsc-conservation-and-tfbs/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "ucsc-conservation-and-tfbs", 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/google-deepmind/science-skills.git --path skills/ucsc_conservation_and_tfbs--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 google-deepmind/science-skills --skill ucsc-conservation-and-tfbs -a gemini-cliProject install goes to .agents/skills/; add -g for ~/.gemini/skills/.
$ gh skill install google-deepmind/science-skills ucsc-conservation-and-tfbs --agent gemini-cliProject scope by default (.agents/skills/); add --scope user for a personal install.
$ git clone --depth 1 https://github.com/google-deepmind/science-skills.git skills-src && mkdir -p .gemini/skills && cp -r skills-src/skills/ucsc_conservation_and_tfbs .gemini/skills/ucsc-conservation-and-tfbs && 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 "ucsc-conservation-and-tfbs" agent skill from https://github.com/google-deepmind/science-skills/tree/main/skills/ucsc_conservation_and_tfbs into .gemini/skills/ucsc-conservation-and-tfbs/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "ucsc-conservation-and-tfbs", 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 google-deepmind/science-skills ucsc-conservation-and-tfbsInstalls 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 google-deepmind/science-skills --skill ucsc-conservation-and-tfbs -a github-copilotProject install goes to .agents/skills/; add -g for ~/.copilot/skills/.
$ git clone --depth 1 https://github.com/google-deepmind/science-skills.git skills-src && mkdir -p .github/skills && cp -r skills-src/skills/ucsc_conservation_and_tfbs .github/skills/ucsc-conservation-and-tfbs && 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 "ucsc-conservation-and-tfbs" agent skill from https://github.com/google-deepmind/science-skills/tree/main/skills/ucsc_conservation_and_tfbs into .github/skills/ucsc-conservation-and-tfbs/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "ucsc-conservation-and-tfbs", 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 google-deepmind/science-skills --skill ucsc-conservation-and-tfbs -a opencodeOpenCode documents no install command of its own. Project install goes to .agents/skills/; add -g for ~/.config/opencode/skills/.
$ gh skill install google-deepmind/science-skills ucsc-conservation-and-tfbs --agent opencodeProject scope by default (.agents/skills/); add --scope user for a personal install.
$ git clone --depth 1 https://github.com/google-deepmind/science-skills.git skills-src && mkdir -p .opencode/skills && cp -r skills-src/skills/ucsc_conservation_and_tfbs .opencode/skills/ucsc-conservation-and-tfbs && 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 "ucsc-conservation-and-tfbs" agent skill from https://github.com/google-deepmind/science-skills/tree/main/skills/ucsc_conservation_and_tfbs into .opencode/skills/ucsc-conservation-and-tfbs/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "ucsc-conservation-and-tfbs", 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.
ucsc-conservation-and-tfbsFetch Evolutionary Conservation scores (phyloP, phastCons) and Transcription Factor Binding Sites (TFBS) from the UCSC Genome Browser.
Ucsc Conservation And Tfbs is an agent skill from google-deepmind/science-skills. Fetch Evolutionary Conservation scores (phyloP, phastCons) and Transcription Factor Binding Sites (TFBS) from the UCSC Genome Browser. Use when analyzing whether genomic variants or regions are evolutionarily conserved, functionally important, or bounded by TF regulators across major projects (ENCODE, JASPAR, ReMap).
Its SKILL.md is about 1.9k tokens, which your agent loads only when the skill is triggered. The skill folder holds 6 other files, including scripts and reference files (for example `scripts/get_conservation.py`, `scripts/get_tfbs.py` and `scripts/list_tracks.py`).
It sits in Research & Science, covering Bioinformatics, Transcription and Browser automation. The repository describes itself as: GDM Science Skills to speed up agentic scientific workflows with better grounding and higher token efficiency. Integrate insights from AlphaGenome, AFDB, UniProt and 30+ other… The licence is Apache-2.0.
2 steps, taken from the first numbered list in SKILL.md.
Read from SKILL.md and the folder at commit 8ab7672. It shows what the files ask for, not the result of running them.
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.
Ships 3 files in scripts/ (Python), which the agent can run.
Shell commands in SKILL.md call:
uvFrom the folder's file list and the shell code blocks in SKILL.md.
Links to these hosts (documentation or services it may open):
genome.ucsc.eduFrom URLs in SKILL.md, links to its own repository left out.
Names no API keys, tokens, secrets or passwords.
From names ending in _API_KEY, _TOKEN, _SECRET, _KEY or _PASSWORD in SKILL.md.
Ucsc Conservation And Tfbs loads about 1.9k tokens when it runs, and up to ~2.1k if it reads all its reference files. Until then it costs about 86 tokens; SKILL.md has 757 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.
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); the scripts in this folder are not scanned.
The full file from google-deepmind/science-skills at commit 8ab7672, republished under its Apache-2.0 licence (© google-deepmind). 757 words, ~1,928 tokens.
.claude/skills/ucsc-conservation-and-tfbs/SKILL.md (or your agent's skills folder). This skill also uses 4 other files; get the full folder from GitHub.This skill provides access to evolutionary constraint scores and conserved
elements from the UCSC Genome Browser. It retrieves scores from the PHAST
package — specifically phastCons (identifying functional blocks) and phyloP
(measuring individual site constraint) — calculated from multiple alignments.
Use this skill to determine if a non-coding variant hits a site that hasn't changed since a common ancestor (which is a strong signal for pathogenicity) or to find conservation peaks across a regulatory element.
uv: Read the uv skill and follow its Setup instructions to ensure
uv is installed and on PATH.This skill includes scripts to query different types of genomic data from UCSC:
scripts/get_conservation.py: For Evolutionary Conservation scores
(phyloP, phastCons).scripts/get_tfbs.py: For Transcription Factor Binding Sites (TFBS).scripts/list_tracks.py: For listing available tracks based on search
or group constraints.Always use the hg38 genome assembly by default, unless the user has specified
otherwise.
To get the evolutionary constraint at a single base, or a list of specific
bases. This is optimal for single nucleotide variants (SNVs). phyloP is the
best metric for individual bases.
uv run scripts/get_conservation.py --coordinates "chr1:215867804" "chr1:215867823" --output /tmp/cons_output.jsonTo identify "conservation peaks" across a non-coding regulatory element (like an
enhancer) to see if an ISM-predicted importance peak aligns with evolutionary
history. phastCons is best for functional windows due to HMM smoothing. The
--conserved-elements flag will also retrieve predefined blocks under extreme
constraint.
uv run scripts/get_conservation.py --coordinates "chr8:11748914-11749085" --conserved-elements --output /tmp/region_cons.jsonYou can control the evolutionary depth using the --collection flag. The
default (vertebrate) uses the 100-vertebrate Multiz alignment for both
hg38 and hg19, matching the UCSC Genome Browser's default comparative genomics
tracks.
vertebrate (default): UCSC 100-vertebrate Multiz alignment. phyloP:
phyloP100way, phastCons: phastCons100way.mammal: Hiller Lab 470-way mammalian alignment. phyloP:
phyloP470wayBW, phastCons: phastCons470way.primate: UCSC 30-primate Multiz alignment. phyloP: phyloP30way,
phastCons: phastCons30way.vertebrate (default): UCSC 100-vertebrate Multiz alignment. phyloP:
phyloP100way, phastCons: phastCons100way.vertebrate46: UCSC 46-vertebrate Multiz alignment (legacy). phyloP:
phyloP46wayAll, phastCons: phastCons46way.mammal: 46-way placental mammal subset. phyloP:
phyloP46wayPlacental, phastCons: phastCons46wayPlacental.primate: 46-way primate subset. phyloP: phyloP46wayPrimates,
phastCons: phastCons46wayPrimates.# hg38 mammal (Hiller 470-way)
uv run scripts/get_conservation.py --coordinates "chr5:1045330-1046172" --collection mammal --output /tmp/mammal_cons.json
# hg19 with legacy 46-vertebrate alignment
uv run scripts/get_conservation.py --coordinates "chr5:1045330-1046172" --genome hg19 --collection vertebrate46 --output /tmp/vert46_cons.jsonTo analyze whether a specific locus is undergoing evolutionary acceleration
(i.e. evolving more rapidly than the neutral drift baseline), use --analyze.
This will compute scalar statistics (mean, min, max) for phyloP scores and
provide a heuristic boolean is_accelerated to simplify your evaluation.
uv run scripts/get_conservation.py --coordinates "chr5:1045330-1046172" --analyze --output /tmp/accelerated_cons.jsonTo identify transcription factor binding sites for a given genomic interval. This is useful for interpreting non-coding variants that might disrupt TF binding.
Run scripts/get_tfbs.py with --coordinates and --tracks. You can query
multiple tracks at once.
uv run scripts/get_tfbs.py --coordinates "chr11:1001000-1010000" --tracks encRegTfbsClustered --output /tmp/tfbs_encode.jsonJASPAR tracks may return very large result sets. Use --tf-filter to keep only
items whose TFName field contains the given substring (case-insensitive):
uv run scripts/get_tfbs.py --coordinates "chr6:36670000-36690000" --tracks jaspar2024 --tf-filter TP53 --output /tmp/tp53_sites.jsonencRegTfbsClustered (TF Clusters)jaspar2026, jaspar2024 (Predicted TFBS)ReMapTFs (ChIP-seq Atlas)[!CAUTION] Tracks like
jasparorReMapwithout years are often "container" tracks and will fail with a 400 error. Always use the specific subtrack name (e.g.,jaspar2026).
To list available tracks (such as different versions of JASPAR, or purely to discover what tracks exist for a particular genome assembly):
uv run scripts/list_tracks.py --search "jaspar" --output /tmp/jaspar_tracks.jsonYou can also filter by functional group:
uv run scripts/list_tracks.py --group "regulation" --output /tmp/regulation_tracks.json--collection mammal) constraint if you are
explicitly looking for deep evolutionary roots across all vertebrates. Use
the default vertebrate collection.© google-deepmind, 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
SKILL.md and 4 other files (scripts, references) in skills/ucsc_conservation_and_tfbs of google-deepmind/science-skills.
Open the folder on GitHubat commit 8ab7672
We found 1 copy of this SKILL.md (exact, near-identical or edited) in other folders, from 1 other GitHub owner. This page covers the copy in google-deepmind/science-skills, which our catalogue first saw on October 7, 2026.
Ucsc Conservation And Tfbs 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 |
|---|---|---|---|---|---|---|
| Ucsc Conservation And Tfbs this skillgoogle-deepmind/science-skills | 3.2k | 1 repos | ~1.9k | Automated safety check: Pass | Apache-2.0 | |
| ArboretoK-Dense-AI/scientific-agent-skills | 48k | 1 repos | ~2.7k | Automated safety check: Pass | BSD-3-Clause | |
| Bio Chipseq Allele Specific BindingGPTomics/bioSkills | 1.2k | 2 repos | ~3.9k | Automated safety check: Pass | MIT | |
| Jaspar DatabaseLeonChaoX/qinyan-academic-skills | 944 | 1 repos | ~3k | Automated safety check: Pass | CC0-1.0 | |
| Bio Gene Regulatory Networks Grn InferenceGPTomics/bioSkills | 1.2k | 1 repos | ~3.5k | Automated safety check: Pass | MIT | |
| Bio Gene Regulatory Networks Perturbation SimulationGPTomics/bioSkills | 1.2k | 1 repos | ~3.6k | Automated safety check: Pass | MIT |
K-Dense-AI/scientific-agent-skills
Infers candidate gene regulatory networks from bulk or single-cell expression data using AertsLab Arboreto GRNBoost2 and GENIE3.
GPTomics/bioSkills
Detects allele-specific transcription factor or histone modification binding from heterozygous-variant ChIP-seq using WASP (reference-bias filter; mandatory upstream), RASQUAL (joint QTL +…
LeonChaoX/qinyan-academic-skills
Query JASPAR for transcription factor binding site (TFBS) profiles (PWMs/PFMs).
GPTomics/bioSkills
Infer gene regulatory networks from bulk or general expression data with mutual-information (ARACNe) and tree-ensemble (GENIE3, GRNBoost2) methods, and infer transcription-factor protein activity…
GPTomics/bioSkills
Simulate transcription factor perturbation effects on cell state in silico with CellOracle and Dynamo, and predict transcriptional responses to genetic perturbations with GEARS, scGen, and CPA.
GPTomics/bioSkills
Designs pegRNAs and nicking guides for prime editing (PE) -- choosing the nick/strand, tuning the primer-binding site (PBS) and reverse-transcription template (RTT) as a per-locus panel, selecting…
google-deepmind/science-skills
Retrieve and analyze AlphaFold predicted structures for a protein.
google-deepmind/science-skills
Analyzes genetic variant effects on gene expression (RNA-seq), chromatin accessibility (DNASE), histone marks (ChIP), and transcription factors using the AlphaGenome API.
google-deepmind/science-skills
Query the ChEMBL database for bioactive molecules, drug targets, bioactivity data, approved drugs, and chemical structures.
google-deepmind/science-skills
Query ClinicalTrials.gov via APIv2. An agent skill from google-deepmind/science-skills.
google-deepmind/science-skills
A skill your agent uses when needing clinical significance, pathogenicity classifications (e.g., Pathogenic, Benign, VUS), clinical evidence rationales, or finding "hard positive" benchmark controls…
google-deepmind/science-skills
A skill your agent uses when you want to look up, map, and search for short genetic variants (SNPs, indels) in NCBI's dbSNP database.
Categories
Fetch Evolutionary Conservation scores (phyloP, phastCons) and Transcription Factor Binding Sites (TFBS) from the UCSC Genome Browser. Ucsc Conservation And Tfbs is an agent skill from google-deepmind/science-skills. Fetch Evolutionary Conservation scores (phyloP, phastCons) and Transcription Factor Binding Sites (TFBS) from the UCSC Genome Browser.
Ucsc Conservation And Tfbs fits situations like: analyzing whether genomic variants; regions are evolutionarily conserved; functionally important; bounded by TF regulators across major projects (ENCODE.
Run `npx skills add google-deepmind/science-skills --skill ucsc-conservation-and-tfbs -a claude-code`. Or copy the skill folder (skills/ucsc_conservation_and_tfbs in google-deepmind/science-skills) into .claude/skills/ucsc-conservation-and-tfbs in your project. Claude Code loads it when a task matches its description.
Run `npx skills add google-deepmind/science-skills --skill ucsc-conservation-and-tfbs -a codex`. Or copy the skill folder (skills/ucsc_conservation_and_tfbs in google-deepmind/science-skills) into .agents/skills/ucsc-conservation-and-tfbs in your project. Codex loads it when a task matches its description.
Cursor, Gemini CLI, GitHub Copilot and OpenCode also load SKILL.md folders. With the skills CLI, run `npx skills add google-deepmind/science-skills --skill ucsc-conservation-and-tfbs -a cursor` (or -a gemini-cli, github-copilot or opencode for the others). To copy it by hand, put the folder in .cursor/skills/ucsc-conservation-and-tfbs, .gemini/skills/ucsc-conservation-and-tfbs, .github/skills/ucsc-conservation-and-tfbs and .opencode/skills/ucsc-conservation-and-tfbs in your project.
Going by SKILL.md and its folder, Ucsc Conservation And Tfbs needs Python for the scripts in its folder and the command-line tools its instructions call (uv). Our summary lists: Python 3.
SKILL.md names 1 domain. As links in the text: genome.ucsc.edu. This is read from the text; nothing was executed.
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. The check reads SKILL.md only: the scripts in the folder are not scanned, so read them before running anything.
Ucsc Conservation And Tfbs is published under the Apache-2.0 licence (the repository's licence). It allows redistribution, so the full SKILL.md is shown on this page.
About 1.9k tokens (SKILL.md is roughly 7.7k characters). Agents keep only the skill's name and description in context until a task matches; then they load SKILL.md in full. Its references folder adds about 203 tokens, read only when the agent opens those files.
Skills that share tags, products or a category with Ucsc Conservation And Tfbs: Arboreto (K-Dense-AI/scientific-agent-skills, 48k stars), Bio Chipseq Allele Specific Binding (GPTomics/bioSkills, 1.2k stars), Jaspar Database (LeonChaoX/qinyan-academic-skills, 944 stars) and Bio Gene Regulatory Networks Grn Inference (GPTomics/bioSkills, 1.2k stars). The comparison table on this page puts their stars, adoption, token cost, safety result and licence side by side.
google-deepmind (a GitHub organization) maintains it in google-deepmind/science-skills, which has 3,233 GitHub stars. The repository holds 40 skills in this directory. The repository was last updated on October 9, 2026.
Source: google-deepmind/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.