ammawla

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

Agent

Execute ENCODE DNase-seq pipeline from FASTQ to hotspots and footprints using BWA, Hotspot2, and HINT-ATAC.

ammawla/encode-toolkit

Agent

Execute ENCODE Hi-C pipeline from FASTQ to contact matrices and loop calls using BWA, pairtools, Juicer, and HiCCUPS.

ammawla/encode-toolkit

Agent

Execute ENCODE RNA-seq pipeline from FASTQ to gene quantification using STAR 2-pass alignment and RSEM/Kallisto.

ammawla/encode-toolkit

Agent

Execute ENCODE WGBS pipeline from FASTQ to methylation calls using Bismark and MethylDackel.

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

Command

Cross-reference ENCODE data with PubMed, GEO, ClinicalTrials, and bioRxiv.

ammawla/encode-toolkit

Command

Download ENCODE files (BED, FASTQ, BAM, bigWig) with MD5 verification.

ammawla/encode-toolkit

Command

Log derived files and trace provenance back to ENCODE source data.

ammawla/encode-toolkit

Command

Store, check, or clear ENCODE API credentials for restricted data.

ammawla/encode-toolkit

Command

Assess ENCODE experiment quality using QC metrics and audit flags.

ammawla/encode-toolkit

Command

Search ENCODE experiments by assay, organ, biosample, or target.

ammawla/encode-toolkit

Command

Track ENCODE experiments locally with publications and provenance.

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

Build comprehensive chromatin accessibility maps by aggregating ATAC-seq and DNase-seq narrowPeak data across multiple ENCODE experiments, donors, and labs. Use when the user wants to answer "where is chromatin accessible in my tissue?" by combining peak calls into a union peak set. Handles cross-lab variation, ATAC…

ammawla/encode-toolkit

Skill Claude CodeCodex

Guide for multi-experiment batch operations: QC screening, batch download, comparison, and report generation across many ENCODE experiments simultaneously. Use when users need to process 5+ experiments together, create experiment comparison tables, perform batch quality checks, or generate summary reports. Trigger on…