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.

Data

encode-toolkit

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

FLOW.md

ammawla@ammawla

GitHub

Stats

Python JavaScript Node Bash GraphQL

What's inside

Skills

/accessibility-aggregationBuild comprehensive chromatin accessibility maps by aggregating ATAC-seq and DNase-seq narrowPeak data across multiple ENCODE experiments, donors, and labs. Use when the user wants to answer "where is chromatin accessible in my tissue?" by combining peak calls into a union peak

FAQ

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.

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.

Flowy

encode-toolkit · Flowy

README

Read on GitHub ↗

ENCODE Toolkit — Genomics Research Infrastructure for Claude

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

Start from ENCODE but go everywhere: discover histone peaks, cross-reference with GWAS variants, check ClinVar pathogenicity, pull GTEx expression, analyze TF binding motifs from JASPAR, run pipelines, and generate publication-ready methods with full provenance — in one conversation.

Citation Notes

If you use ENCODE-Toolkit, please cite:

Alex M. Mawla. (2026). ENCODE-Toolkit: an MCP server, Claude plugin, and skills suite for ENCODE genomic data access and analysis. Zenodo. https://doi.org/10.5281/zenodo.18917511

BibTeX

@software{mawla_2026_encode_toolkit,
  author  = {Mawla, Alex M.},
  title   = {ENCODE-Toolkit: an MCP server, Claude plugin, and skills suite for ENCODE genomic data access and analysis},
  year    = {2026},
  publisher = {Zenodo},
  doi     = {10.5281/zenodo.18917511},
  url     = {https://doi.org/10.5281/zenodo.18917511}
}

Quick Start

Claude Code Plugin (recommended)

Start a new Claude Code session and enter:

/plugin marketplace add ammawla/encode-toolkit

/plugin install encode-toolkit

That's it. All 20 tools, 47 skills, and the MCP connector are now available.

If you only need the 20 MCP tools without the 47 workflow skills:

claude mcp add encode -- uvx encode-toolkit

npx (Node.js)

npx encode-toolkit

Or in MCP client config: { "command": "npx", "args": ["encode-toolkit"] }

pip install

pip install encode-toolkit

Then use encode-toolkit as the command in any MCP client configuration:

{
  "mcpServers": {
    "encode": {
      "command": "encode-toolkit"
    }
  }
}

Add to your claude_desktop_config.json:

macOS: ~/Library/Application Support/Claude/claude_desktop_config.json Windows: %APPDATA%\Claude\claude_desktop_config.json

{
  "mcpServers": {
    "encode": {
      "command": "uvx",
      "args": ["encode-toolkit"]
    }
  }
}

No installation needed when using uvx. Just add the config and restart Claude.

Add to .vscode/mcp.json in your workspace:

{
  "mcp": {
    "servers": {
      "encode": {
        "command": "uvx",
        "args": ["encode-toolkit"]
      }
    }
  }
}

Add to .cursor/mcp.json:

{
  "mcpServers": {
    "encode": {
      "command": "uvx",
      "args": ["encode-toolkit"]
    }
  }
}

Add to .windsurf/mcp.json:

{
  "mcpServers": {
    "encode": {
      "command": "uvx",
      "args": ["encode-toolkit"]
    }
  }
}

Connected Databases

ENCODE Toolkit integrates 14 databases through live API tools and guided skills.

Database	Access Method	Use Case
ENCODE	20 MCP tools (live API)	ChIP-seq, ATAC-seq, RNA-seq, Hi-C, WGBS, CUT&RUN data
GTEx	REST API (skill)	Tissue-specific gene expression across 54 tissues
ClinVar	E-utilities (skill)	Variant clinical significance and pathogenicity
GWAS Catalog	REST API (skill)	Trait-variant associations from genome-wide studies
JASPAR	REST API (skill)	Transcription factor binding motif profiles
CellxGene	Census API (skill)	Single-cell expression atlas across tissues
gnomAD	GraphQL (skill)	Population allele frequencies and gene constraint
Ensembl	REST API (skill)	VEP annotation, Regulatory Build, coordinate liftover
UCSC Genome Browser	REST API (skill)	cCRE tracks, TF clusters, sequence retrieval
GEO	E-utilities (skill)	Complementary expression/epigenomic datasets
PubMed	MCP server	Literature search and citation
bioRxiv	MCP server	Preprint discovery
ClinicalTrials.gov	MCP server	Clinical trial cross-reference
Open Targets	MCP server	Drug target identification

What You Can Ask Claude

Search and explore

"Find all histone ChIP-seq experiments for human pancreas tissue"
"What ATAC-seq data is available for mouse brain?"
"Search for RNA-seq on GM12878 cell line"
"What histone marks have ChIP-seq data for pancreas?"

Download and track

"Download all BED files from ENCSR133RZO to ~/data/encode"
"Track experiment ENCSR133RZO with its publications"
"Export citations for my tracked experiments as BibTeX"

Cross-reference databases

"What GWAS variants overlap islet enhancers?"
"Check ClinVar pathogenicity for rs7903146"
"Pull GTEx expression for TCF7L2 across tissues"
"Find JASPAR motifs for HNF4A binding sites"

Run pipelines

"Set up a ChIP-seq pipeline for my H3K27ac experiments"
"Run ATAC-seq analysis with ENCODE-standard QC thresholds"

Generate methods and provenance

"Log that I created filtered_peaks.bed from ENCSR133RZO using bedtools"
"Generate a methods section for my analysis with citations"

Experiment details

"Show me the full details for experiment ENCSR133RZO"
"What files are available for ENCSR133RZO?"
"List only the BED files from ENCSR133RZO"

Bulk downloads

"Download all FASTQs from human pancreas ChIP-seq to /data/fastqs"
"Get the IDR thresholded peaks from these experiments"
"Download the bigWig signal tracks for H3K27me3 in GRCh38"

Compatibility analysis

"Are experiments ENCSR133RZO and ENCSR000AKS compatible for combined analysis?"
"Compare these two ChIP-seq experiments"

Provenance chains

"Show me the provenance chain for my derived files"
"What files have I derived from ENCSR133RZO?"

The Problem

Using genomics databases today means:

Navigate web portals, click through dozens of filters
Manually find the right experiments and files across multiple databases
Write custom scripts to batch download
Lose track of which files came from where

With ENCODE Toolkit, just tell Claude what you need:

"Find all histone ChIP-seq data for human pancreas tissue"

Claude searches ENCODE, returns a structured table of 66 experiments with targets, replicates, and file counts. Downloads are organized by experiment with MD5 verification and full provenance tracking.

Available Tools (20)

Five core tools are shown below. The remaining 15 are collapsed for readability.

`encode_search_experiments`

Search ENCODE experiments with 20+ filters.

Parameter	Type	Description
`assay_title`	string	Assay type: "Histone ChIP-seq", "ATAC-seq", "RNA-seq", "Hi-C", etc.
`organism`	string	Species (default: "Homo sapiens")
`organ`	string	Organ: "pancreas", "brain", "liver", "heart", "kidney", etc.
`biosample_type`	string	"tissue", "cell line", "primary cell", "organoid"
`target`	string	ChIP target: "H3K27me3", "H3K4me3", "CTCF", etc.
`biosample_term_name`	string	Specific biosample: "GM12878", "HepG2", etc.
`limit`	int	Max results (default: 25)

`encode_get_experiment`

Get full details for a single experiment including all files, quality metrics, and audit info.

Parameter	Type	Description
`accession`	string	Experiment ID (e.g., "ENCSR133RZO")

`encode_download_files`

Download specific files by accession to a local directory.

Parameter	Type	Description
`file_accessions`	list[str]	File IDs to download (e.g., ["ENCFF635JIA"])
`download_dir`	string	Local path to save files
`organize_by`	string	"flat", "experiment", "format", "experiment_format"
`verify_md5`	bool	Verify file integrity (default: true)

`encode_batch_download`

Search + download in one step. Runs in preview mode by default.

Parameter	Type	Description
`download_dir`	string	Local path to save files
`file_format`	string	File format to download
`assay_title`	string	Assay type filter
`organ`	string	Organ filter
`dry_run`	bool	Preview only (default: true). Set false to download.

`encode_track_experiment`

Track an experiment locally with its publications, methods, and pipeline info.

Parameter	Type	Description
`accession`	string	Experiment ID to track
`fetch_publications`	bool	Fetch associated publications (default: true)
`fetch_pipelines`	bool	Fetch pipeline/analysis info (default: true)
`notes`	string	Optional notes to attach

`encode_list_files`

List files for a specific experiment with format/type filters.

Parameter	Type	Description
`experiment_accession`	string	Experiment ID
`file_format`	string	"fastq", "bam", "bed", "bigWig", "bigBed", etc.
`output_type`	string	"reads", "peaks", "signal", "alignments", etc.
`assembly`	string	"GRCh38", "mm10", etc.
`preferred_default`	bool	Only return recommended files

`encode_search_files`

Search files across all experiments with combined experiment + file filters.

Parameter	Type	Description
`file_format`	string	File format filter
`assay_title`	string	Assay type of parent experiment
`organ`	string	Organ of parent experiment
`target`	string	ChIP/CUT&RUN target
`output_type`	string	Output type filter
`assembly`	string	Genome assembly

`encode_get_metadata`

List valid filter values for any parameter.

Parameter	Type	Description
`metadata_type`	string	"assays", "organisms", "organs", "biosample_types", "file_formats", "output_types", "assemblies"

`encode_get_facets`

Get live counts from ENCODE showing what data exists for given filters.

Parameter	Type	Description
`assay_title`	string	Pre-filter by assay
`organism`	string	Pre-filter by organism
`organ`	string	Pre-filter by organ

`encode_get_file_info`

Get detailed metadata for a single file.

Parameter	Type	Description
`accession`	string	File ID (e.g., "ENCFF635JIA")

`encode_manage_credentials`

Store, check, or clear ENCODE credentials for restricted data access.

Parameter	Type	Description
`action`	string	"store", "check", or "clear"
`access_key`	string	ENCODE access key (for "store")
`secret_key`	string	ENCODE secret key (for "store")

`encode_list_tracked`

List all experiments in your local tracker with metadata, publication counts, and derived file counts.

Parameter	Type	Description
`assay_title`	string	Filter by assay type
`organism`	string	Filter by organism
`organ`	string	Filter by organ

`encode_get_citations`

Get publications for tracked experiments. Export as BibTeX or RIS for reference managers.

Parameter	Type	Description
`accession`	string	Specific experiment (or all if omitted)
`export_format`	string	"json" (default), "bibtex", or "ris"

`encode_compare_experiments`

Analyze whether two experiments are compatible for combined analysis.

Parameter	Type	Description
`accession1`	string	First experiment ID
`accession2`	string	Second experiment ID

`encode_summarize_collection`

Get grouped statistics of your tracked experiment collection.

Parameter	Type	Description
`assay_title`	string	Filter by assay type
`organism`	string	Filter by organism
`organ`	string	Filter by organ

`encode_log_derived_file`

Log a file you created from ENCODE data for provenance tracking.

Parameter	Type	Description
`file_path`	string	Path to your derived file
`source_accessions`	list[str]	ENCODE accessions this was derived from
`description`	string	What the file contains
`tool_used`	string	Tool/software used
`parameters`	string	Command or parameters used

`encode_get_provenance`

View provenance chains from derived files back to source ENCODE data.

Parameter	Type	Description
`file_path`	string	Get provenance for a specific file
`source_accession`	string	List all files derived from an accession

`encode_export_data`

Export tracked experiments as a table (CSV, TSV, or JSON) for Excel, R, pandas.

Parameter	Type	Description
`format`	string	"csv" (default), "tsv", or "json"
`assay_title`	string	Filter by assay type

`encode_link_reference`

Link external references (PubMed, bioRxiv, ClinicalTrials, GEO) to tracked experiments.

Parameter	Type	Description
`experiment_accession`	string	ENCODE experiment accession
`reference_type`	string	"pmid", "doi", "nct_id", "preprint_doi", "geo_accession", "other"
`reference_id`	string	The identifier value

`encode_get_references`

Get external references linked to tracked experiments for cross-server workflows.

Parameter	Type	Description
`experiment_accession`	string	Filter by experiment (optional)
`reference_type`	string	Filter by type (optional)

Authentication

Most ENCODE data is public and requires no authentication. Just install and use.

For restricted/unreleased data, ask Claude: "Store my ENCODE credentials"

Credentials are encrypted using your OS keyring (macOS Keychain, Linux Secret Service, Windows Credential Locker) and never stored in plaintext. Get your access keys from your ENCODE profile.

Plugin Skills (47)

When installed as a Claude Code plugin, ENCODE Toolkit includes 47 literature-backed workflow skills that guide Claude through complex genomics tasks. Each analysis skill includes evidence-based quality thresholds, assay-specific metrics, and citations to primary literature.

Core Skills

Skill	Description
`setup`	Install and configure the ENCODE Toolkit server
`search-encode`	Search and explore ENCODE experiments and files
`download-encode`	Download files with organization and verification
`track-experiments`	Track experiments, citations, and provenance locally
`cross-reference`	Connect ENCODE data to PubMed, bioRxiv, ClinicalTrials.gov

Skill	Description
`quality-assessment`	Evaluate experiment quality using ENCODE metrics — assay-specific thresholds for ChIP-seq (FRiP, NSC, RSC, NRF, IDR), ATAC-seq (TSS enrichment, NFR ratio), RNA-seq (mapping rate, gene body coverage), WGBS (bisulfite conversion, CpG coverage), Hi-C (cis/trans ratio), and CUT&RUN/CUT&Tag. Backed by Landt 2012, Buenrostro 2013, ENCODE Phase 3 (2020), Li 2011
`integrative-analysis`	Combine multiple experiments with batch effect awareness — integration strategies (peak overlap, signal correlation, DiffBind, DESeq2, ChromHMM, ABC model). Backed by Ernst & Kellis 2012, Ross-Innes 2012, Love 2014, Fulco 2019
`regulatory-elements`	Discover enhancers, promoters, insulators from combinatorial histone marks — ENCODE cCRE classification (926,535 elements), ChromHMM state interpretation. Backed by ENCODE Phase 3 (2020), Roadmap Epigenomics (2015), Whyte 2013
`epigenome-profiling`	Build comprehensive chromatin state profiles — three-tiered histone panels, ChromHMM 15-state model, bivalent chromatin analysis. References the chromatin biology catalog
`compare-biosamples`	Compare experiments across tissues and cell types — biosample hierarchy, tissue-specific regulation, batch effect detection. Backed by Roadmap Epigenomics (2015), Leek 2010
`visualization-workflow`	Generate publication-quality visualizations: genome browser tracks, heatmaps, and signal profiles
`motif-analysis`	Discover and analyze TF binding motifs in regulatory regions using HOMER, MEME, and JASPAR
`peak-annotation`	Annotate genomic peaks with features (promoter/enhancer/intergenic), nearest genes, and functional categories
`batch-analysis`	Batch processing and QC screening across multiple ENCODE experiments with systematic quality filtering

Skill	Description
`functional-screen-analysis`	Analyze CRISPR screens, MPRA, and STARR-seq data from ENCODE — MAGeCK, BAGEL2, MPRAflow integration

Skill	Description
`histone-aggregation`	Union merge of histone ChIP-seq peaks across studies — signalValue-based noise filtering, sample-of-origin tagging, ENCODE blacklist removal. Backed by ChIP-Atlas (Oki 2018), Amemiya 2019, Perna 2024
`accessibility-aggregation`	Union merge of ATAC-seq and DNase-seq peaks — cross-platform integration, peak summit preservation. Backed by Corces 2017, Amemiya 2019, Zhao 2020
`hic-aggregation`	Union catalog of Hi-C chromatin loops (BEDPE) — resolution-aware anchor matching, loop caller concordance tracking. Backed by Loop Catalog (Reyna 2025), Mustache (Roayaei Ardakany 2020)
`methylation-aggregation`	Aggregate WGBS methylation profiles — per-CpG weighted averaging, HMR/UMR/PMD identification. Backed by Schultz 2015, DMRcate (Peters 2021), Zhou 2020

Skill	Description
`scrna-meta-analysis`	Cross-study meta-analysis of scRNA-seq data — reproducibility assessment, TIN-based quality filtering, ambient RNA quantification. Backed by Tran 2020, Luecken & Theis 2019, Stuart 2019, Korsunsky 2019
`multi-omics-integration`	Integrate RNA-seq, ATAC-seq, Histone ChIP-seq, and TF ChIP-seq — ABC model regulatory predictions, signal correlation. Backed by Fulco 2019, Corces 2018, ENCODE Phase 3 (2020)

Skill	Description
`data-provenance`	Full reproducibility tracking — tool versions, reference files, scripts, exact commands, timestamps, source-to-derived provenance chains
`cite-encode`	Generate proper citations, BibTeX/RIS export, data availability statements
`variant-annotation`	Annotate GWAS/disease variants with ENCODE functional data — variant-to-gene mapping via cCREs. Backed by Finucane 2015, Maurano 2012
`pipeline-guide`	Understand ENCODE uniform analysis pipelines and output types — pipeline specifications, Nextflow integration
`single-cell-encode`	Work with scRNA-seq and scATAC-seq data — platform comparison, cross-study integration, WNN multimodal analysis. Backed by Hao 2021, Stuart 2019
`disease-research`	Disease-focused workflows — GWAS variant interpretation, disease-tissue mapping, heritability enrichment, drug target identification via Open Targets. Backed by Buniello 2019, Finucane 2015
`publication-trust`	Publication integrity assessment — 5-level trust scoring, retraction/erratum detection, citation analysis. Integrates with PubMed, bioRxiv, and Consensus
`bioinformatics-installer`	Install all bioinformatics tools for ENCODE analyses — 7 conda environment YAMLs, 3 install scripts, 134+ tools across ChIP-seq, ATAC-seq, RNA-seq, WGBS, Hi-C, DNase-seq, CUT&RUN
`scientific-writing`	Generate publication-ready methods sections, figure legends, supplementary tables, and data availability statements with full tool citations
`liftover-coordinates`	Convert genomic coordinates between assembly versions (hg19/hg38, mm9/mm10) using UCSC liftOver, CrossMap, Ensembl REST API, and rtracklayer

Skill	Description
`gtex-expression`	Query GTEx tissue expression data via REST API for gene expression context across 54 tissues
`clinvar-annotation`	Annotate variants with ClinVar clinical significance, pathogenicity, and review status
`cellxgene-context`	Query CellxGene single-cell atlas for cell type expression context across tissues
`gwas-catalog`	Search NHGRI-EBI GWAS Catalog for trait associations, risk alleles, and study metadata
`jaspar-motifs`	Query JASPAR database for transcription factor binding motifs and matrix profiles
`ensembl-annotation`	Ensembl VEP variant annotation, Regulatory Build, coordinate liftover, gene lookup via REST API
`geo-connector`	Search NCBI GEO for complementary datasets, cross-reference with ENCODE, FTP downloads
`gnomad-variants`	gnomAD population allele frequencies, gene constraint (LOEUF/pLI), structural variants via GraphQL
`ucsc-browser`	UCSC Genome Browser REST API for cCRE tracks, TF binding clusters, and sequence retrieval

Pipeline	Assay	Aligner	Caller
`pipeline-chipseq`	ChIP-seq	BWA-MEM	MACS2 + IDR
`pipeline-atacseq`	ATAC-seq	Bowtie2	MACS2 (Tn5-adjusted)
`pipeline-rnaseq`	RNA-seq	STAR	RSEM + Kallisto
`pipeline-wgbs`	WGBS	Bismark	MethylDackel
`pipeline-hic`	Hi-C	BWA	Juicer + HiCCUPS
`pipeline-dnaseseq`	DNase-seq	BWA	Hotspot2
`pipeline-cutandrun`	CUT&RUN	Bowtie2	SEACR

Each pipeline includes a SKILL.md overview, 5-stage reference files (preprocessing through QC), a complete Nextflow DSL2 pipeline, a Dockerfile, and deployment configurations for local, SLURM, GCP, and AWS.

File	Description
`skills/histone-aggregation/references/histone-marks-reference.md`	Comprehensive chromatin biology catalog (1,442 lines) — 21 histone marks with writers/erasers/readers, 5 novel acylation marks, ChromHMM state models (5 to 51 states), TF co-binding patterns, chromatin remodeling complexes, DNA methylation-chromatin interplay, nucleosome dynamics, 3D genome organization, chromatin in disease. 74 primary references
`skills/*/references/literature.md`	33 per-skill literature reference documents — ~250 papers cataloged with DOI, PMID, citation counts, and skill-relevant key findings

Why ENCODE Toolkit

Most genomics tools give you one thing. ENCODE Toolkit gives you the full research loop:

Capability	ENCODE Toolkit	Typical MCP servers
Live database access	20 tools across 14 databases	Single database, read-only
Executable pipelines	7 Nextflow DSL2 pipelines with Docker and cloud configs	None
Provenance tracking	Full audit trail from source data to derived files	None
Publication output	BibTeX/RIS citations, auto-generated methods sections	None
Literature backing	100+ primary references with assay-specific QC thresholds	None
Workflow skills	47 guided skills covering search to publication	Static documentation

Supported Assay Types

Category	Assays
Histone/Chromatin	Histone ChIP-seq, TF ChIP-seq, ATAC-seq, DNase-seq, CUT&RUN, CUT&Tag, MNase-seq
Transcription	RNA-seq, total RNA-seq, small RNA-seq, long read RNA-seq, CAGE, RAMPAGE, PRO-seq, GRO-seq
3D Genome	Hi-C, intact Hi-C, Micro-C, ChIA-PET, HiChIP, PLAC-seq, 5C
DNA Methylation	WGBS, RRBS, MeDIP-seq, MRE-seq
Functional	STARR-seq, MPRA, CRISPR screen, eCLIP, iCLIP
Single Cell	scRNA-seq, snATAC-seq, 10x multiome, SHARE-seq, Parse SPLiT-seq
Perturbation	CRISPRi + RNA-seq, shRNA + RNA-seq, siRNA + RNA-seq

Supported file formats: fastq bam bed bigWig bigBed tsv csv hic tagAlign bedpe pairs fasta vcf tar

Security and Privacy

100% local execution — no telemetry, no analytics, no tracking
Credentials encrypted at rest via OS keyring with Fernet fallback
Certificate verification enforced — no verify=False
Rate limited to respect ENCODE's 10 req/sec policy
MD5 verification on all downloads by default
No data leaves your machine except queries to public APIs over HTTPS

Vignettes

Step-by-step walkthroughs showing real Claude sessions, including actual API output and scientific interpretation.

Vignette	Skills Demonstrated
01 — Discovery & Search	Facets, search, metadata, quality-aware selection
02 — Download & Track	File listing, download, tracking, citations, provenance
03 — Epigenomics Workflow	Histone marks, ATAC-seq, aggregation skills
04 — Variant & Disease Research	GWAS catalog, ClinVar, GTEx, JASPAR, gnomAD
05 — Expression & Single-Cell	RNA-seq, scRNA-seq, GTEx, CellxGene, meta-analysis
06 — Motif & Regulatory Analysis	TF ChIP-seq, chromatin states, HOMER/MEME
07 — 3D Genome & Methylation	Hi-C loops, WGBS methylation, integrative analysis
08 — Pipeline Execution	ChIP-seq/ATAC-seq/RNA-seq pipelines, Nextflow
09 — Cross-Reference & Integration	GEO, PubMed, Ensembl, UCSC, multi-omics

Every skill has a dedicated vignette in docs/skill-vignettes/ with a complete example session. Highlights:

Skill	Vignette Scenario
data-provenance	Download, blacklist-filter, liftover, auto-generate methods section
histone-aggregation	Union merge of H3K27ac across 5 pancreas experiments
variant-annotation	rs7903146 in TCF7L2 with islet enhancer evidence scoring
pipeline-chipseq	Full Nextflow pipeline execution with ENCODE QC thresholds
gwas-catalog	T2D GWAS variants overlaid on islet H3K27ac enhancers
publication-trust	Trust assessment of artemisinin transdifferentiation claim
scrna-meta-analysis	3-study islet integration following Mawla et al. 2019 framework

See the full showcase for 15 detailed examples.

Development

git clone https://github.com/ammawla/encode-toolkit.git
cd encode-toolkit
python -m venv .venv
source .venv/bin/activate
pip install -e ".[dev]"

Run the server locally:

encode-toolkit

Run tests:

pytest

Troubleshooting

Make sure you restarted Claude Desktop after adding the config
Verify uvx is installed: pip install uv or curl -LsSf https://astral.sh/uv/install.sh | sh

Check your internet connection
ENCODE API rate limit is 10 requests/sec — the server handles this automatically

The file may require authentication. Ask Claude: "Store my ENCODE credentials"
Or check if the file status is "released" on encodeproject.org

Try broader filters (remove biosample_type or organ)
Use encode_get_facets to see what data actually exists for your filters
Use encode_get_metadata to check valid filter values

Author

Dr. Alex M. Mawla, PhD

License

AGPL-3.0. See LICENSE for full terms.

For commercial licensing inquiries: ammawla@ucdavis.edu

File tree

498

ammawla/encode-toolkitView on GitHub ↗

.claude/
.claude-plugin/
  marketplace.json
  plugin.json
  settings.json
.cursor-plugin/
  marketplace.json
  plugin.json
.env.example
.github/
  dependabot.yml
  ISSUE_TEMPLATE/
    bug_report.yml
    feature_request.yml
  PULL_REQUEST_TEMPLATE.md
  workflows/
    clone-count.yml
    lint.yml
    release.yml
    test.yml
    validate.yml
.gitignore
.mcp.json
.pre-commit-config.yaml
agents/
  atacseq-pipeline.md
  chipseq-pipeline.md
  cutandrun-pipeline.md
  dnaseseq-pipeline.md
  hic-pipeline.md
  rnaseq-pipeline.md
  wgbs-pipeline.md
CHANGELOG.md
CITATION.cff
CLAUDE.md
commands/
  browse-files.md
  cite-encode.md
  compare-experiments.md
  cross-reference.md
  download-encode.md
  log-provenance.md
  manage-credentials.md
  quality-check.md
  search-encode.md
  track-experiments.md
conftest.py
CONTRIBUTING.md
Dockerfile
docs/
  api-reference.md
  icon.svg
  integrations.md
  security.md
  SHOWCASE.md
  skill-vignettes/
    accessibility-aggregation.md
    batch-analysis.md
    cellxgene-context.md
    cite-encode.md
    clinvar-annotation.md
    compare-biosamples.md
    cross-reference.md
    data-provenance.md
    disease-research.md
    download-encode.md
    ensembl-annotation.md
    epigenome-profiling.md
    geo-connector.md
    gnomad-variants.md
    gtex-expression.md
    gwas-catalog.md
    hic-aggregation.md
    histone-aggregation.md
    integrative-analysis.md
    jaspar-motifs.md
    methylation-aggregation.md
    motif-analysis.md
    multi-omics-integration.md
    peak-annotation.md
    pipeline-atacseq.md
    pipeline-chipseq.md
    pipeline-cutandrun.md
    pipeline-dnaseseq.md
    pipeline-guide.md
    pipeline-hic.md
    pipeline-rnaseq.md
    pipeline-wgbs.md
    publication-trust.md
    quality-assessment.md
    regulatory-elements.md
    scrna-meta-analysis.md
    search-encode.md
    setup.md
    single-cell-encode.md
    track-experiments.md
    ucsc-browser.md
    variant-annotation.md
    visualization-workflow.md
  submission-examples.md
  vignettes/
    _captured_output.md
    01-discovery-and-search.md
    02-download-and-track.md
    03-epigenomics-workflow.md
    04-variant-and-disease.md
    05-expression-and-single-cell.md
    06-motif-and-regulatory.md
    07-3d-genome-and-methylation.md
    08-pipeline-execution.md
    09-cross-reference-and-integration.md
  walkthrough.md
glama.json
index.js
LICENSE
package.json
plugin/
  .claude-plugin/
    plugin.json
  .mcp.json
  agents/
    atacseq-pipeline.md
    chipseq-pipeline.md
    cutandrun-pipeline.md
    dnaseseq-pipeline.md
    hic-pipeline.md
    rnaseq-pipeline.md
    wgbs-pipeline.md
  CLAUDE.md
  commands/
    browse-files.md
    cite-encode.md
    compare-experiments.md
    cross-reference.md
    download-encode.md
    log-provenance.md
    manage-credentials.md
    quality-check.md
    search-encode.md
    track-experiments.md
  skills/
    accessibility-aggregation/
      references/
        atac-vs-dnase.md
        literature.md
      scripts/
        validate_peaks.py
      SKILL.md
    batch-analysis/
      references/
        literature.md
      SKILL.md
    bioinformatics-installer/
      environments/
        atacseq-env.yml
        chipseq-env.yml
        cutandrun-env.yml
        dnaseseq-env.yml
        hic-env.yml
        rnaseq-env.yml
        wgbs-env.yml
      references/
        literature.md
      scripts/
        install-nextflow.sh
        install-python-packages.sh
        install-r-packages.R
      SKILL.md
    cellxgene-context/
      references/
        literature.md
      SKILL.md
    cite-encode/
      references/
        literature.md
      SKILL.md
    clinvar-annotation/
      references/
        literature.md
      SKILL.md
    compare-biosamples/
      references/
        literature.md
      SKILL.md
    cross-reference/
      references/
        literature.md
      SKILL.md
    data-provenance/
      references/
        literature.md
      SKILL.md
    disease-research/
      references/
        literature.md
      SKILL.md
    download-encode/
      references/
        literature.md
      SKILL.md
    ensembl-annotation/
      references/
        literature.md
      SKILL.md
    epigenome-profiling/
      references/
        literature.md
      SKILL.md
    functional-screen-analysis/
      references/
        literature.md
      SKILL.md
    geo-connector/
      references/
        literature.md
      SKILL.md
    gnomad-variants/
      references/
        literature.md
      SKILL.md
    gtex-expression/
      references/
        literature.md
      SKILL.md
    gwas-catalog/
      references/
        literature.md
      SKILL.md
    hic-aggregation/
      references/
        literature.md
        loop-caller-comparison.md
      scripts/
        validate_loops.py
      SKILL.md
    histone-aggregation/
      references/
        broad-vs-narrow.md
        histone-marks-reference.md
        literature.md
        signal-filtering.md
      scripts/
        validate_peaks.py
      SKILL.md
    integrative-analysis/
      references/
        literature.md
      SKILL.md
    jaspar-motifs/
      references/
        literature.md
      SKILL.md
    liftover-coordinates/
      references/
        literature.md
      SKILL.md
    methylation-aggregation/
      references/
        hmr-definitions.md
        literature.md
      scripts/
        validate_methylation.py
      SKILL.md
    motif-analysis/
      references/
        literature.md
      SKILL.md
    multi-omics-integration/
      references/
        literature.md
      SKILL.md
    peak-annotation/
      references/
        literature.md
      SKILL.md
    pipeline-atacseq/
      references/
        01-qc-trimming.md
        02-alignment.md
        03-tn5-filtering.md
        04-peak-calling.md
        05-qc-metrics.md
        literature.md
      scripts/
        Dockerfile
        main.nf
        nextflow.config
      SKILL.md
    pipeline-chipseq/
      references/
        01-qc-trimming.md
        02-alignment.md
        03-filtering.md
        04-analysis.md
        05-qc-metrics.md
        literature.md
      scripts/
        Dockerfile
        main.nf
        nextflow.config
      SKILL.md
    pipeline-cutandrun/
      references/
        01-qc-trimming.md
        02-bowtie2-alignment.md
        03-filtering-spikein.md
        04-seacr-peaks.md
        05-qc-metrics.md
        literature.md
      scripts/
        Dockerfile
        main.nf
        nextflow.config
      SKILL.md
    pipeline-dnaseseq/
      references/
        01-qc-trimming.md
        02-alignment.md
        03-filtering.md
        04-hotspot-calling.md
        05-footprinting.md
        literature.md
      scripts/
        Dockerfile
        main.nf
        nextflow.config
      SKILL.md
    pipeline-guide/
      references/
        literature.md
      SKILL.md
    pipeline-hic/
      references/
        01-qc-trimming.md
        02-alignment.md
        03-pair-processing.md
        04-matrix-generation.md
        05-loop-calling.md
        literature.md
      scripts/
        Dockerfile
        main.nf
        nextflow.config
      SKILL.md
    pipeline-rnaseq/
      references/
        01-qc-trimming.md
        02-star-alignment.md
        03-quantification.md
        04-signal-tracks.md
        05-qc-metrics.md
        literature.md
      scripts/
        Dockerfile
        main.nf
        nextflow.config
      SKILL.md
    pipeline-wgbs/
      references/
        01-qc-trimming.md
        02-bismark-alignment.md
        03-dedup-filtering.md
        04-methylation-calling.md
        05-qc-metrics.md
        literature.md
      scripts/
        Dockerfile
        main.nf
        nextflow.config
      SKILL.md
    publication-trust/
      references/
        literature.md
      SKILL.md
    quality-assessment/
      references/
        literature.md
      SKILL.md
    regulatory-elements/
      references/
        literature.md
      SKILL.md
    scientific-writing/
      references/
        literature.md
      SKILL.md
    scrna-meta-analysis/
      references/
        literature.md
      SKILL.md
    search-encode/
      references/
        literature.md
      SKILL.md
    setup/
      references/
        literature.md
      SKILL.md
    single-cell-encode/
      references/
... 335 more

encode-toolkit

Skills

encode-toolkit

Skills

Agents

Commands

Badges

README

ENCODE Toolkit — Genomics Research Infrastructure for Claude

Citation Notes

BibTeX

Quick Start

Claude Code Plugin (recommended)

npx (Node.js)

pip install

Connected Databases

What You Can Ask Claude

Search and explore

Download and track

Cross-reference databases

Run pipelines

Generate methods and provenance

Experiment details

Bulk downloads

Compatibility analysis

Provenance chains

The Problem

Available Tools (20)

encode_search_experiments

encode_get_experiment

encode_download_files

encode_batch_download

encode_track_experiment

encode_list_files

encode_search_files

encode_get_metadata

encode_get_facets

encode_get_file_info

encode_manage_credentials

encode_list_tracked

encode_get_citations

encode_compare_experiments

encode_summarize_collection

encode_log_derived_file

encode_get_provenance

encode_export_data

encode_link_reference

encode_get_references

Authentication

Plugin Skills (47)

Core Skills

Why ENCODE Toolkit

Supported Assay Types

Security and Privacy

Vignettes

Development

Troubleshooting

Author

License

File tree

`encode_search_experiments`

`encode_get_experiment`

`encode_download_files`

`encode_batch_download`

`encode_track_experiment`

`encode_list_files`

`encode_search_files`

`encode_get_metadata`

`encode_get_facets`

`encode_get_file_info`

`encode_manage_credentials`

`encode_list_tracked`

`encode_get_citations`

`encode_compare_experiments`

`encode_summarize_collection`

`encode_log_derived_file`

`encode_get_provenance`

`encode_export_data`

`encode_link_reference`

`encode_get_references`