# ammawla/encode-toolkit [Health: Active]

**Category:** Biology, Medicine and Bioinformatics  
**Repository:** https://github.com/ammawla/encode-toolkit  
**GitHub Stars:** 24  
**Views:** 3  
**Installs:** 0  
**Upvotes:** 0  
**Directory Page:** https://allmcps.com/mcp/ammawla-encode-toolkit

## Description
MCP server and Claude Plugin for a full ENCODE Project genomic data and analysis toolkit — search, download, track, and analyze functional genomics experiments.

## Tools
Capabilities this server exposes over MCP:

- **encode_search_experiments** — Search ENCODE experiments with 20+ filters.
- **encode_get_experiment** — Get full details for a single experiment including all files, quality metrics, and audit info.
- **encode_download_files** — Download specific files by accession to a local directory.
- **encode_batch_download** — Search + download in one step. Runs in preview mode by default.
- **encode_track_experiment** — Track an experiment locally with its publications, methods, and pipeline info.
- **encode_list_files** — List files for a specific experiment with format/type filters.
- **encode_search_files** — Search files across all experiments with combined experiment + file filters.
- **encode_get_metadata** — List valid filter values for any parameter.
- **encode_get_facets** — Get live counts from ENCODE showing what data exists for given filters.
- **encode_get_file_info** — Get detailed metadata for a single file.
- **encode_manage_credentials** — Store, check, or clear ENCODE credentials for restricted data access.
- **encode_list_tracked** — List all experiments in your local tracker with metadata, publication counts, and derived file counts.
- **encode_get_citations** — Get publications for tracked experiments. Export as BibTeX or RIS for reference managers.
- **encode_compare_experiments** — Analyze whether two experiments are compatible for combined analysis.
- **encode_summarize_collection** — Get grouped statistics of your tracked experiment collection.
- **encode_log_derived_file** — Log a file you created from ENCODE data for provenance tracking.
- **encode_get_provenance** — View provenance chains from derived files back to source ENCODE data.
- **encode_export_data** — Export tracked experiments as a table (CSV, TSV, or JSON) for Excel, R, pandas.
- **encode_link_reference** — Link external references (PubMed, bioRxiv, ClinicalTrials, GEO) to tracked experiments.
- **encode_get_references** — Get external references linked to tracked experiments for cross-server workflows.

## Claude Desktop Quick Installation
Install path detected from listing signals. Uses `uvx` (confidence: high):

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

## Documentation

## What ammawla/encode-toolkit MCP server does

ammawla/encode-toolkit MCP server connects an MCP-compatible client to the ENCODE Project for genomic data discovery and local research organization. Its tools cover experiment searches, experiment details, file listings, file metadata, downloads, and filter metadata. The server can also maintain a local tracker for experiments and record relationships between source ENCODE files and derived outputs.

The repository describes support for common functional genomics data types, including ChIP-seq, ATAC-seq, RNA-seq, Hi-C, WGBS, and CUT&RUN. Beyond ENCODE’s live API tools, the project includes skills that guide work with databases such as GTEx, ClinVar, GWAS Catalog, JASPAR, CellxGene, gnomAD, Ensembl, UCSC Genome Browser, GEO, PubMed, bioRxiv, ClinicalTrials.gov, and Open Targets. These connected systems are presented as skills or MCP integrations rather than as the core ENCODE tool set.

## How it works

Search tools accept experiment and file filters, while metadata and facet tools help identify valid filter values and show available-data counts. After an experiment is selected, the client can retrieve its files, quality information, audit details, publications, methods, and pipeline information. Downloads can target selected accessions or combine a search with a download operation; batch download starts in preview mode by default.

Local tracking supports collection-level workflows. Tracked experiments can be compared for combined-analysis compatibility, summarized statistically, exported as CSV, TSV, or JSON, and used to produce BibTeX or RIS citations. External references from sources including PubMed, bioRxiv, ClinicalTrials.gov, and GEO can be linked to tracked experiments. Derived files can be logged with their source data so provenance chains can be inspected later.

## Setup and configuration

The README documents a Python 3.10-or-newer project and provides a direct MCP-only command using uvx:

```bash
uvx encode-toolkit
```

Claude Desktop, Cursor, and Windsurf configurations use the same `uvx` command with `encode-toolkit` as its argument. The README also documents installation through pip and an npx-based configuration. A Claude Code plugin is available through the project’s marketplace commands and includes the MCP connector plus workflow skills.

The server includes a credential-management tool for storing, checking, or clearing ENCODE credentials when restricted data access is needed. The supplied material does not specify environment variables or a required credential format, so configuration details for authenticated access should be checked in the project documentation.

## Tools and capabilities

The documented MCP tools support:

- Searching experiments and files with combined filters.
- Retrieving experiment, file, audit, quality, and facet metadata.
- Listing files by experiment, format, or type.
- Downloading individual files or previewing batch downloads.
- Tracking experiments and listing tracked collections.
- Exporting tracked data as CSV, TSV, or JSON.
- Comparing experiments for combined analysis.
- Exporting tracked publications as BibTeX or RIS.
- Logging derived files and inspecting provenance chains.
- Linking and retrieving external references.

## Limitations and notes

The project is marked beta in the supplied README. Its live MCP tools are centered on ENCODE, while many additional databases are accessed through guided skills or separate MCP integrations. The material does not establish that every listed database is directly exposed as an MCP tool by this server. Restricted ENCODE data may require credentials, but public-data access and the exact authentication requirements are not specified here.

ammawla/encode-toolkit MCP server is licensed under AGPL-3.0. The README also identifies the project as having no telemetry and documents a full provenance workflow, but users should verify current behavior and version-specific details before relying on those properties in a production research process.

_Full upstream README: https://allmcps.com/mcp/ammawla-encode-toolkit/readme_