tooluniverse-epigenomics
Skill1.1k starsChanged 8 months agoNo licenceView on GitHub
Production-ready genomics and epigenomics data processing for BixBench questions. Handles methylation array analysis (CpG filtering, differential methylation, age-related CpG detection, chromosome-level density), ChIP-seq peak analysis (peak calling, motif enrichment, coverage stats), ATAC-seq chromatin accessibility, multi-omics integration (expression + methylation correlation), and genome-wide statistics. Pure Python computation (pandas, scipy, numpy, pysam, statsmodels) plus ToolUniverse annotation tools (Ensembl, ENCODE, SCREEN, JASPAR, ReMap, RegulomeDB, ChIPAtlas). Supports BED, BigWig, methylation beta-value matrices, Illumina manifest files, and multi-sample clinical data. Use when processing methylation data, ChIP-seq peaks, ATAC-seq signals, or answering questions about CpG sites, differential methylation, chromatin accessibility, histone marks, or epigenomic statistics.
We split this skill into the rules it gives an agent
15 rules. About 0 are common, 13 are distinctive, and 2 are very specific to this project.
≈0
Common · estimate
Many files like this have a rule of this kind.
≈13
Distinctive · estimate
This author's own choices. Worth a look.
2
Very specific
Tied to their project's names, files or tools. Probably skip.
No licence file, so all rights are reserved — read it at the source. We count its rules but don't quote them. Read them on GitHub.
≈ “Common” is an estimate: at least 1 in 5 of the 308,232 skill files we read have a rule of the same kind, not the same words. “Very specific” is our guess from the words: it names a file, a command, a setting or the project itself.
Trending
More talk lately.thin dataabout the whole repository
Who's talking about wu-yc/LabClaw
- rpatrik96/research-agora“Interested in contributing from Tübingen + relevant reference”GitHub · Mar 31, 2026 · 1 reactions
- sudosubin/agents.nix“agent-skills.github.wu-yc.labclaw: init at 0-unstable-2026-03-19”GitHub · Oct 4, 2026
The biggest 2 of 2 mentions linking to the repository that our crawl found. Each line is their own headline.
In this repository239 other files it gives its agents.
- alphafold-databaseSkill
- analyze_lab_video_cell_behaviorSkill
- anndataSkill
- arboretoSkill
- benchling-integrationSkill
- bioinformaticsSkill
- biomniSkill
- biopythonSkill
- brenda-databaseSkill
- cellxgene-censusSkill
- clinpgx-databaseSkill
- cobrapySkill
- cosmic-databaseSkill
- deeptoolsSkill
- detect_common_wetlab_errorsSkill
- dnanexus-integrationSkill
- egocentric_view_to_structured_logSkill
- ena-databaseSkill
- ensembl-databaseSkill
- esmSkill
- etetoolkitSkill
- extract_experiment_data_from_videoSkill
- flowioSkill
- gene-databaseSkill
- genimlSkill
- geo-databaseSkill
- ggetSkill
- gtarsSkill
- gwas-databaseSkill
- histolabSkill
- hmdb-databaseSkill
- hypogenicSkill
- kegg-databaseSkill
- labarchive-integrationSkill
- lamindbSkill
- latchbio-integrationSkill
- matchmsSkill
- metabolomics-workbench-databaseSkill
- omero-integrationSkill
- opentrons-integrationSkill
- pathmlSkill
- pdb-databaseSkill
- protocolsio-integrationSkill
- protocol_video_matchingSkill
- pydeseq2Skill
- pylabrobotSkill
- pyopenmsSkill
- pysamSkill
- reactome-databaseSkill
- realtime_protocol_guidance_promptsSkill
- robot_protocol_step_generatorSkill
- scanpySkill
- scikit-bioSkill
- scikit-survivalSkill
- scvi-toolsSkill
- string-databaseSkill
- tooluniverse-crispr-screen-analysisSkill
- tooluniverse-expression-data-retrievalSkill
- tooluniverse-gene-enrichmentSkill
- tooluniverse-gwas-drug-discoverySkill
- The first 60 shown.
Does it work?
Reviews from people and from AI agents that ran it: what they used it for, and whether it worked.
Reviews can't be read right now.
Your trail
Files you open will collect here, so you can find them again.
Open two or more, and you can remix the rules you like from each into one list. Kept in this browser only.
Now do this for your own.
Bring your CLAUDE.md, AGENTS.md or skills. agentleFS shows which of your rules are common, which are yours and which only fit one project, and keeps one version your agents read everywhere.