# encode-toolkit

Search ENCODE, cross-reference 14 databases, run 7 analysis pipelines, and generate publication-ready methods — all from natural language in Claude Code.

- Tier: Indexed (plain plugin)
- Category: Data
- Page: https://www.flowy.sh/listings/ammawla-encode-toolkit
- Source: https://github.com/ammawla/encode-toolkit
- Price: free and open source

## Summary
encode-toolkit is a Claude Code plugin with 94 hand-picked skills for data work, indexed on Flowy. Install it with the command on its page. It includes accessibility-aggregation, batch-analysis, bioinformatics-installer. Its skills do not fire on their own yet. Request auto-invocation to have Flowy route them as you prompt. Free and open source.

## Install (Claude Code)
```
npx -y skills add ammawla/encode-toolkit
```

## Skills
- accessibility-aggregation
- batch-analysis
- bioinformatics-installer
- cellxgene-context
- cite-encode
- clinvar-annotation
- compare-biosamples
- cross-reference
- data-provenance
- disease-research
- download-encode
- ensembl-annotation
- epigenome-profiling
- functional-screen-analysis
- geo-connector
- gnomad-variants
- gtex-expression
- gwas-catalog
- hic-aggregation
- histone-aggregation
- integrative-analysis
- jaspar-motifs
- liftover-coordinates
- methylation-aggregation
- motif-analysis
- multi-omics-integration
- peak-annotation
- pipeline-atacseq
- pipeline-chipseq
- pipeline-cutandrun
- pipeline-dnaseseq
- pipeline-guide
- pipeline-hic
- pipeline-rnaseq
- pipeline-wgbs
- publication-trust
- quality-assessment
- regulatory-elements
- scientific-writing
- scrna-meta-analysis
- search-encode
- setup
- single-cell-encode
- track-experiments
- ucsc-browser
- variant-annotation
- visualization-workflow
- accessibility-aggregation
- batch-analysis
- bioinformatics-installer
- cellxgene-context
- cite-encode
- clinvar-annotation
- compare-biosamples
- cross-reference
- data-provenance
- disease-research
- download-encode
- ensembl-annotation
- epigenome-profiling
- functional-screen-analysis
- geo-connector
- gnomad-variants
- gtex-expression
- gwas-catalog
- hic-aggregation
- histone-aggregation
- integrative-analysis
- jaspar-motifs
- liftover-coordinates
- methylation-aggregation
- motif-analysis
- multi-omics-integration
- peak-annotation
- pipeline-atacseq
- pipeline-chipseq
- pipeline-cutandrun
- pipeline-dnaseseq
- pipeline-guide
- pipeline-hic
- pipeline-rnaseq
- pipeline-wgbs
- publication-trust
- quality-assessment
- regulatory-elements
- scientific-writing
- scrna-meta-analysis
- search-encode
- setup
- single-cell-encode
- track-experiments
- ucsc-browser
- variant-annotation
- visualization-workflow

## FAQ

### What is encode-toolkit?
Search ENCODE, cross-reference 14 databases, run 7 analysis pipelines, and generate publication-ready methods — all from natural language in Claude Code.

### How do I install encode-toolkit?
Run these in Claude Code: npx -y skills add ammawla/encode-toolkit. Then prompt normally.

### Does encode-toolkit auto-invoke its skills?
Not yet. It is indexed on Flowy as a plain plugin. Request auto-invocation on its page and Flowy will route its skills for you as you prompt.

### Is encode-toolkit free?
Yes. Flowy is free and open source, with nothing gated. You can read every skill in full before you install.