v0.3.0

What's Changed

• Bump actions/setup-node from 4 to 6 by @dependabot[bot] in #1
• Bump actions/checkout from 4 to 6 by @dependabot[bot] in #2
• Bump actions/upload-artifact from 4 to 7 by @dependabot[bot] in #3

New Contributors

• @dependabot[bot] made their first contribution in #1

Full Changelog: v0.3.0-beta.10...v0.3.0

v0.3.0-beta.10

Changes

License Update

• CC-BY-NC-ND-4.0 → CC-BY-NC-4.0: Now allows forks and contributions while blocking commercial monetization
• Encourages academic, research, and personal use
• Citation requirement via Zenodo DOI
• Contributor license terms for PRs

Download Badges

• PyPI weekly downloads badge (690/week)
• npm weekly downloads badge (596/week)

Clone Tracking

• GitHub Actions workflow for daily clone count accumulation
• Requires SECRET_TOKEN repo secret (classic PAT with repo + gist scopes)

Version

• Bumped to 0.3.0-beta.10 across all 8 manifest files

Full Changelog: v0.3.0-beta.9...v0.3.0-beta.10

v0.3.0-beta.9

What's New

Cursor Plugin Compatibility

Install encode-toolkit in Cursor via .cursor-plugin/ manifest:

• Full plugin.json + marketplace.json manifests
• 4 Cursor rules (.mdc): data quality, provenance, API patterns, file formats
• MCP server auto-configuration

Commands (10)

Quick-action entry points covering all 20 MCP tools:

• search-encode, download-encode, browse-files, track-experiments
• quality-check, cite-encode, cross-reference, compare-experiments
• manage-credentials, log-provenance

Pipeline Agents (7)

Multi-step pipeline execution agents:

• ChIP-seq (BWA-MEM → MACS2 → IDR)
• ATAC-seq (Bowtie2 → Tn5 shift → MACS2)
• RNA-seq (STAR 2-pass → RSEM → Kallisto)
• WGBS (Bismark → MethylDackel)
• Hi-C (BWA → pairtools → Juicer → HiCCUPS)
• DNase-seq (BWA → Hotspot2 → HINT-ATAC)
• CUT&RUN (Bowtie2 → SEACR → spike-in)

Pre-commit Hooks

• OS file blocker (.DS_Store, Thumbs.db)
• Case conflict and merge conflict detection
• Ruff lint + format, mypy, YAML/JSON validation

Housekeeping

• .gitignore cleaned up, local-only entries moved to .git/info/exclude
• Version 0.3.0-beta.9 across all 8 manifest files

Full Plugin Contents

• 20 MCP tools (ENCODE API)
• 47 workflow skills
• 10 commands
• 7 pipeline agents
• 4 Cursor rules
• 7 Nextflow pipelines
• 14 database integrations

Full Changelog: v0.3.0-beta.8...v0.3.0-beta.9

v0.3.0-beta.8

What's New

Marketplace Plugin Install

Install encode-toolkit directly in Claude Code:

/plugin marketplace add ammawla/encode-toolkit
/plugin install encode-toolkit

Changes

• Marketplace plugin structure — plugin/ directory with real files (not symlinks) for marketplace install
• MCP connector — .mcp.json enables the Connectors section in the plugin UI
• Fixed skill descriptions — 18 skills using YAML >- block scalar now display properly
• README Quick Start — marketplace install is now the recommended method
• Accurate skill count — 47 skills (tabaseq-deconvolution is unreleased)
• Version consistency — all 8 manifest files aligned at 0.3.0-beta.8

Full Plugin Contents

• 20 MCP tools (ENCODE API)
• 47 workflow skills
• 1 MCP connector
• 7 Nextflow pipelines
• 14 database integrations

Full Changelog: v0.3.0-beta.6...v0.3.0-beta.8

v0.3.0-beta.6

Full Changelog: v0.3.0-beta.5...v0.3.0-beta.6

v0.3.0-beta.5

Full Changelog: v0.3.0-beta.4...v0.3.0-beta.5

Full Changelog: v0.3.0-beta.4...v0.3.0-beta.5

v0.3.0-beta.4

Full Changelog: v0.3.0-beta.3...v0.3.0-beta.4

Full Changelog: v0.3.0-beta.3...v0.3.0-beta.4

v0.3.0-beta.3

Full Changelog: v0.3.0-beta.2...v0.3.0-beta.3

v0.3.0-beta.2

ENCODE Toolkit v0.3.0-beta.2

MCP server for the ENCODE Project — 20 tools, 47 skills, 14 database integrations, and 7 analysis pipelines for genomics research in Claude Code.

Highlights

• 20 MCP tools: Search, download, track, compare, and cross-reference ENCODE data
• 47 expert skills: Analysis workflows, pipeline execution, external database integration
• 14 databases: ENCODE, PubMed, bioRxiv, ClinicalTrials.gov, Open Targets, GTEx, ClinVar, GWAS Catalog, JASPAR, gnomAD, Ensembl, UCSC, GEO, CELLxGENE
• 7 Nextflow pipelines: ChIP-seq, ATAC-seq, RNA-seq, WGBS, Hi-C, DNase-seq, CUT&RUN
• Full provenance tracking: SQLite-backed experiment tracking with publications and citations
• MD5 verification: All file downloads verified for integrity

Install

claude mcp add encode -- uvx encode-toolkit

Links

• PyPI
• npm
• Documentation