ai-bio instructions

ammawla/encode-toolkit

Plugin Claude Code

Plugin marketplace listing 1 plugin: encode-toolkit.

ammawla/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.

ammawla/encode-toolkit

Settings file Claude Code

Agent settings declaring 5 allowed tools.

ammawla/encode-toolkit

Instructions file

Claude Code instructions for ammawla/encode-toolkit, covering encode toolkit, quick start, source architecture, package identity and development gotchas.

ammawla/encode-toolkit

Agent

Execute ENCODE ATAC-seq pipeline from FASTQ to accessibility peaks with Tn5 correction, Bowtie2, and MACS2.

ammawla/encode-toolkit

Agent

Execute ENCODE ChIP-seq pipeline from FASTQ to peaks and signal tracks using BWA-MEM, MACS2, and IDR.

ammawla/encode-toolkit

Agent

Execute CUT&RUN pipeline from FASTQ to peaks with Bowtie2, SEACR, and spike-in normalization.

ammawla/encode-toolkit

Command

List, search, and inspect ENCODE files by format, type, and assembly.

ammawla/encode-toolkit

Command

Generate ENCODE citations for publications, grants, and presentations.

ammawla/encode-toolkit

Command

Check if two ENCODE experiments are compatible for combined analysis.

ammawla/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.

ammawla/encode-toolkit

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.

ammawla/encode-toolkit

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…

ammawla/encode-toolkit

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…

ammawla/encode-toolkit

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.