Plugin Claude Code
Plugin marketplace listing 1 plugin: encode-toolkit.
60 tagged ai-bio, measured the same way as everything else here.
Plugin Claude Code
Plugin marketplace listing 1 plugin: encode-toolkit.
Plugin Claude Code
20 ENCODE API tools + 47 expert skills for genomics research. Search experiments, download files with MD5 verification, run pipelines, and cross-reference 14 databases.
Settings file Claude Code
Agent settings declaring 5 allowed tools.
Instructions file
Claude Code instructions for ammawla/encode-toolkit, covering encode toolkit, quick start, source architecture, package identity and development gotchas.
Agent
Execute ENCODE ATAC-seq pipeline from FASTQ to accessibility peaks with Tn5 correction, Bowtie2, and MACS2.
Agent
Execute ENCODE ChIP-seq pipeline from FASTQ to peaks and signal tracks using BWA-MEM, MACS2, and IDR.
Agent
Execute CUT&RUN pipeline from FASTQ to peaks with Bowtie2, SEACR, and spike-in normalization.
Command
List, search, and inspect ENCODE files by format, type, and assembly.
Command
Generate ENCODE citations for publications, grants, and presentations.
Command
Check if two ENCODE experiments are compatible for combined analysis.
Plugin Claude Code
20 ENCODE API tools + 47 expert skills for genomics research. Search experiments, download files with MD5 verification, run pipelines, and cross-reference 14 databases.
Skill Claude CodeCodex
Generate proper ENCODE citations for publications, grants, and presentations. Use when the user needs to cite ENCODE data, create bibliography entries, write acknowledgment sections, or ensure compliance with ENCODE data use policy.
Skill Claude CodeCodex
Cross-reference ENCODE data with PubMed, bioRxiv, ClinicalTrials.gov, Open Targets, GTEx, ClinVar, GWAS Catalog, gnomAD, Ensembl, and other scientific databases. Use when the user wants to find publications, preprints, or clinical trials related to ENCODE experiments, chain ENCODE data with other scientific MCP…
Skill Claude CodeCodex
Build comprehensive epigenomic profiles for tissues or cell types using ENCODE data. Use when the user wants to characterize chromatin states, assemble histone modification panels, create epigenomic landscapes, run ChromHMM segmentation, identify super-enhancers or bivalent domains, profile regulatory elements across…
MCP server Claude CodeCodexCursor +2
20 MCP tools + 48 skills for ENCODE Project genomics — search, download, pipelines. Runs locally from the encode-toolkit npm package.
At most 3 mods per repository are shown here — the rest are on their repository pages: