How does it handle effective genome sizes?

The skill includes built-in references for common assemblies such as GRCh38 (Human), GRCm38 (Mouse), and dm6 (Drosophila) to simplify normalization.

What types of NGS data can this skill handle?

This skill is optimized for ChIP-seq, RNA-seq, ATAC-seq, and MNase-seq data processing, normalization, and visualization.

Is it compatible with standard bioinformatics file formats?

Yes, it is designed to work with standard formats including BAM, bigWig, BED, and bedGraph files.

Does this skill support sequencing normalization?

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

Can I generate plots using this Claude skill?

Absolutely. It helps you generate the necessary commands for creating heatmaps, profile plots, PCA plots, and correlation matrices.

deepTools NGS Analysis

Name: deepTools NGS Analysis
Author: BbgnsurfTech

byBbgnsurfTech

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Ciencia de Datos y ML

Provides a comprehensive suite of tools for processing, normalizing, and visualizing high-throughput sequencing data like ChIP-seq and RNA-seq.

The deepTools skill empowers Claude to assist bioinformaticians and researchers in processing Next-Generation Sequencing (NGS) data through expert guidance on command-line operations. It facilitates the conversion of BAM alignments to normalized bigWig tracks, the execution of rigorous quality control assessments like PCA and fingerprinting, and the generation of publication-quality visualizations including heatmaps and profile plots. By integrating domain-specific knowledge on effective genome sizes and normalization methods such as RPGC and RPKM, this skill ensures accurate, reproducible, and standardized analysis for ChIP-seq, RNA-seq, and ATAC-seq experiments.

Características Principales

01Support for ChIP-seq, RNA-seq, and ATAC-seq workflows

02Comprehensive quality control (PCA, correlation, fingerprints)

03Effective genome size references for major organisms

04Automated BAM to bigWig conversion and normalization

05Publication-ready heatmap and profile plot generation

063 GitHub stars

Casos de Uso

01Visualizing signal enrichment around Transcription Start Sites (TSS)

02Assessing the quality and enrichment of ChIP-seq replicates

03Generating normalized coverage tracks for genomic visualization

What are Skills?·How to Install

Install with 🐟 Skill.Fish

npx skillfish add bbgnsurftech/claude-skills-collection deeptools

For use in Claude.ai and ChatGPT

Download Skill