What sequencing data types does the deepTools skill support?

The deepTools skill supports a wide range of high-throughput sequencing data, including ChIP-seq, RNA-seq, ATAC-seq, and MNase-seq.

How do I validate my genomic input files?

The skill includes a validation script to check for file existence, proper BAM indexing (.bai files), and BED format correctness before starting analysis.

Does it support ATAC-seq specific processing?

Absolutely. It includes workflows for Tn5 transposase offset correction using alignmentSieve and fragment size distribution analysis.

Can this skill help with data normalization?

Yes, it provides guidance and command generation for various normalization methods such as RPGC (1x genome coverage), CPM, RPKM, and BPM.

deepTools NGS Analysis

Name: deepTools NGS Analysis
Author: K-Dense-AI

byK-Dense-AI

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3,718

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数据科学与机器学习

Facilitates comprehensive Next-Generation Sequencing (NGS) data processing, quality control, and publication-quality visualization.

deepTools is a specialized skill for Claude Code that streamlines the analysis of high-throughput sequencing data such as ChIP-seq, RNA-seq, and ATAC-seq. It provides researchers and bioinformaticians with automated workflows for converting BAM files to normalized coverage tracks, performing rigorous quality control assessments like PCA and correlation analysis, and generating detailed heatmaps or profile plots around genomic features. By integrating domain-specific best practices and normalization methods like RPGC and CPM, this skill ensures reproducible and accurate genomic data interpretation directly through Claude's interface.

主要功能

01Built-in file validation for BAM, bigWig, and BED formats to ensure data integrity

02Comprehensive QC suite including PCA, correlation plots, and fingerprint analysis

03Specialized workflows for ChIP-seq, ATAC-seq (Tn5 correction), and strand-specific RNA-seq

04High-quality visualization for heatmaps and profile plots around TSS or peaks

053,718 GitHub stars

06Automated BAM to bigWig conversion with advanced normalization options (RPGC, CPM, RPKM)

使用场景

01Visualizing signal distributions around genomic regions for publication-ready figures

02Performing quality control checks on sequencing replicates to ensure high correlation and depth

03Generating normalized coverage tracks and comparing treatment versus control enrichment

What are Skills?·How to Install

Install with 🐟 Skill.Fish

npx skillfish add k-dense-ai/claude-scientific-skills deeptools

For use in Claude.ai and ChatGPT

Download Skill