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Update SKILL.md files to add double quotation marks for all skills, ensuring clarity and consistency across all entries.

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Haoxuan "Orion" Li
2025-10-20 20:51:50 -07:00
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scientific-packages/deeptools/SKILL.md
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---
name: deeptools
description: deepTools is a comprehensive Python toolkit for analyzing next-generation sequencing (NGS) data including ChIP-seq, RNA-seq, ATAC-seq, MNase-seq, and other genomic experiments. Use this skill for: converting BAM files to bigWig/bedGraph coverage tracks with normalization (RPGC, CPM, RPKM); quality control analysis including sample correlation, PCA, fingerprint plots, coverage assessment, and fragment size analysis; creating heatmaps and profile plots around genomic features like TSS, gene bodies, or peak regions; comparing samples using log2 ratios and correlation analysis; enrichment analysis and peak region visualization; normalization and scaling of sequencing data; publication-quality visualization generation for genomic datasets. Key tools include bamCoverage, bamCompare, computeMatrix, plotHeatmap, plotProfile, plotFingerprint, plotCorrelation, multiBamSummary, and alignmentSieve. Essential for ChIP-seq quality control, RNA-seq coverage analysis, ATAC-seq processing with Tn5 correction, sample comparison workflows, and generating standardized genomic visualizations. Use when working with BAM files, bigWig files, BED region files, or when users request genomic data analysis, quality control assessment, sample correlation, heatmap generation, profile plotting, or publication-ready visualizations for sequencing experiments.
description: "deepTools is a comprehensive Python toolkit for analyzing next-generation sequencing (NGS) data including ChIP-seq, RNA-seq, ATAC-seq, MNase-seq, and other genomic experiments. Use this skill for: converting BAM files to bigWig/bedGraph coverage tracks with normalization (RPGC, CPM, RPKM); quality control analysis including sample correlation, PCA, fingerprint plots, coverage assessment, and fragment size analysis; creating heatmaps and profile plots around genomic features like TSS, gene bodies, or peak regions; comparing samples using log2 ratios and correlation analysis; enrichment analysis and peak region visualization; normalization and scaling of sequencing data; publication-quality visualization generation for genomic datasets. Key tools include bamCoverage, bamCompare, computeMatrix, plotHeatmap, plotProfile, plotFingerprint, plotCorrelation, multiBamSummary, and alignmentSieve. Essential for ChIP-seq quality control, RNA-seq coverage analysis, ATAC-seq processing with Tn5 correction, sample comparison workflows, and generating standardized genomic visualizations. Use when working with BAM files, bigWig files, BED region files, or when users request genomic data analysis, quality control assessment, sample correlation, heatmap generation, profile plotting, or publication-ready visualizations for sequencing experiments."
---
# deepTools: NGS Data Analysis Toolkit