ammawla/encode-toolkit
MCP server and Claude Plugin for a full ENCODE Project genomic data and analysis toolkit — search, download, track, and analyze functional genomics experiments
ARCHETYPE
Skill Collector
Ten-plus skills loaded on demand. A procedural-knowledge library.
Copy this rig
# review before running: this installs third-party code $ claude mcp add encode-toolkit -- npx -y encode-toolkit@latest $ npx degit ammawla/encode-toolkit/skills ./rig-encode-toolkit/skills
MCP servers are added to Claude Code at local scope; env vars are shown as YOUR_… placeholders — we never store values. Files are fetched with degit into a separate folder so you can review before merging.
$ claude mcp add encode-toolkit -- npx -y encode-toolkit@latest $ npx degit ammawla/encode-toolkit/plugin/skills/accessibility-aggregation .claude/skills/accessibility-aggregation $ npx degit ammawla/encode-toolkit/plugin/skills/batch-analysis .claude/skills/batch-analysis $ npx degit ammawla/encode-toolkit/plugin/skills/bioinformatics-installer .claude/skills/bioinformatics-installer $ npx degit ammawla/encode-toolkit/plugin/skills/cellxgene-context .claude/skills/cellxgene-context $ npx degit ammawla/encode-toolkit/plugin/skills/cite-encode .claude/skills/cite-encode $ npx degit ammawla/encode-toolkit/plugin/skills/clinvar-annotation .claude/skills/clinvar-annotation $ npx degit ammawla/encode-toolkit/plugin/skills/compare-biosamples .claude/skills/compare-biosamples $ npx degit ammawla/encode-toolkit/plugin/skills/cross-reference .claude/skills/cross-reference $ npx degit ammawla/encode-toolkit/plugin/skills/data-provenance .claude/skills/data-provenance $ npx degit ammawla/encode-toolkit/plugin/skills/disease-research .claude/skills/disease-research $ npx degit ammawla/encode-toolkit/plugin/skills/download-encode .claude/skills/download-encode $ npx degit ammawla/encode-toolkit/plugin/skills/ensembl-annotation .claude/skills/ensembl-annotation $ npx degit ammawla/encode-toolkit/plugin/skills/epigenome-profiling .claude/skills/epigenome-profiling $ npx degit ammawla/encode-toolkit/plugin/skills/functional-screen-analysis .claude/skills/functional-screen-analysis $ npx degit ammawla/encode-toolkit/plugin/skills/geo-connector .claude/skills/geo-connector $ npx degit ammawla/encode-toolkit/plugin/skills/gnomad-variants .claude/skills/gnomad-variants $ npx degit ammawla/encode-toolkit/plugin/skills/gtex-expression .claude/skills/gtex-expression $ npx degit ammawla/encode-toolkit/plugin/skills/gwas-catalog .claude/skills/gwas-catalog $ npx degit ammawla/encode-toolkit/plugin/skills/hic-aggregation .claude/skills/hic-aggregation $ npx degit ammawla/encode-toolkit/plugin/skills/histone-aggregation .claude/skills/histone-aggregation $ npx degit ammawla/encode-toolkit/plugin/skills/integrative-analysis .claude/skills/integrative-analysis $ npx degit ammawla/encode-toolkit/plugin/skills/jaspar-motifs .claude/skills/jaspar-motifs $ npx degit ammawla/encode-toolkit/plugin/skills/liftover-coordinates .claude/skills/liftover-coordinates $ npx degit ammawla/encode-toolkit/plugin/skills/methylation-aggregation .claude/skills/methylation-aggregation $ npx degit ammawla/encode-toolkit/plugin/skills/motif-analysis .claude/skills/motif-analysis $ npx degit ammawla/encode-toolkit/plugin/skills/multi-omics-integration .claude/skills/multi-omics-integration $ npx degit ammawla/encode-toolkit/plugin/skills/peak-annotation .claude/skills/peak-annotation $ npx degit ammawla/encode-toolkit/plugin/skills/pipeline-atacseq .claude/skills/pipeline-atacseq $ npx degit ammawla/encode-toolkit/plugin/skills/pipeline-chipseq .claude/skills/pipeline-chipseq $ npx degit ammawla/encode-toolkit/plugin/skills/pipeline-cutandrun .claude/skills/pipeline-cutandrun $ npx degit ammawla/encode-toolkit/plugin/skills/pipeline-dnaseseq .claude/skills/pipeline-dnaseseq $ npx degit ammawla/encode-toolkit/plugin/skills/pipeline-guide .claude/skills/pipeline-guide $ npx degit ammawla/encode-toolkit/plugin/skills/pipeline-hic .claude/skills/pipeline-hic $ npx degit ammawla/encode-toolkit/plugin/skills/pipeline-rnaseq .claude/skills/pipeline-rnaseq $ npx degit ammawla/encode-toolkit/plugin/skills/pipeline-wgbs .claude/skills/pipeline-wgbs $ npx degit ammawla/encode-toolkit/plugin/skills/publication-trust .claude/skills/publication-trust $ npx degit ammawla/encode-toolkit/plugin/skills/quality-assessment .claude/skills/quality-assessment $ npx degit ammawla/encode-toolkit/plugin/skills/regulatory-elements .claude/skills/regulatory-elements $ npx degit ammawla/encode-toolkit/plugin/skills/scientific-writing .claude/skills/scientific-writing $ npx degit ammawla/encode-toolkit/plugin/skills/scrna-meta-analysis .claude/skills/scrna-meta-analysis
This rig commits no guardrails. Here is the community baseline instead — the deny/ask rules most often found across all 7,204 rigs:
{
"permissions": {
"deny": [
"Read(./.env)",
"Read(**/.env)",
"Read(~/.ssh/**)",
"Bash(rm -rf *)",
"Read(**/*.pem)",
"Bash(rm -rf /)",
"Bash(git push --force:*)",
"Bash(sudo *)",
"Read(.env)",
"Bash(rm -rf /*)",
"Read(./.env.*)",
"Read(~/.aws/**)",
"Bash(git push --force*)",
"Bash(rm -rf:*)",
"Read(**/*.key)",
"Read(**/.env.*)",
"Bash(sudo:*)",
"Bash(git reset --hard*)",
"Bash(git reset --hard:*)",
"Read(.env.*)"
],
"ask": [
"Bash(git push:*)",
"Bash(git push *)",
"Bash(git commit:*)",
"Bash(rm *)",
"Bash(rm:*)",
"Bash(git rebase *)",
"Bash(wget *)",
"Bash(npm publish:*)",
"Bash(git commit *)",
"Bash(gh pr merge *)"
]
}
} MCP servers (1)
| server | source | est. tokens |
|---|---|---|
| encode-toolkit | npm | 2.5k |
Skills (47)
accessibility-aggregationbatch-analysisbioinformatics-installercellxgene-contextcite-encodeclinvar-annotationcompare-biosamplescross-referencedata-provenancedisease-researchdownload-encodeensembl-annotationepigenome-profilingfunctional-screen-analysisgeo-connectorgnomad-variantsgtex-expressiongwas-cataloghic-aggregationhistone-aggregationintegrative-analysisjaspar-motifsliftover-coordinatesmethylation-aggregationmotif-analysismulti-omics-integrationpeak-annotationpipeline-atacseqpipeline-chipseqpipeline-cutandrunpipeline-dnaseseqpipeline-guidepipeline-hicpipeline-rnaseqpipeline-wgbspublication-trustquality-assessmentregulatory-elementsscientific-writingscrna-meta-analysissearch-encodesetupsingle-cell-encodetrack-experimentsucsc-browservariant-annotationvisualization-workflow
Similar rigs
nizos/tdd-guard
Automated TDD enforcement for Claude Code
Minimalist 1.3k tok ·
terranc/claude-telegram-bot-bridge
A lightweight Telegram bot that bridges Claude Code to any local folder, with autostart support for remote mobile development.
Minimalist 2.1k tok ·
stefanoginella/aicontainer
Sandboxed devcontainer for running Claude Code, Codex, and OpenCode in bypass / auto-approve mode.
Pragmatist 13.0k tok ·
MrTig-afk/claude-remote
Claude Code on your PC, started from your phone, with your full setup intact.
Pragmatist 2.8k tok ·