Convert BAM to bigWig and generate QC visualizations for NGS data.
npx skills add https://github.com/rubensliv/k-dense-ai --skill deeptools-rubensliv
Please help me install this Agent Skill. Skill: deeptools Source: https://github.com/rubensliv/k-dense-ai/tree/main/scientific-skills/deeptools Command: npx skills add https://github.com/rubensliv/k-dense-ai --skill deeptools-rubensliv
deepTools provides an end-to-end toolkit for processing and visualizing next-generation sequencing (NGS) data, simplifying conversion of read alignments into normalized coverage tracks and generating QC metrics and publication-quality visualizations.
Generate a starter workflow with the generator using your BAM files.
High-intent search queries and answers about installing and using this skill.
Convert BAM files to bigWig for ChIP-seq and ATAC-seq visualization by using the bamCoverage tool to transform read alignments into normalized coverage tracks. This Skill orchestrates the end-to-end conversion process and prepares the output for downstream plotting.
The best way to generate publication-ready heatmaps from NGS data is using computeMatrix to calculate scores across genomic regions, followed by plotHeatmap to render the visualizations. This Skill integrates both steps to produce comparative heatmap profiles around genomic features.
Perform QC on RNA-seq and ChIP-seq samples by using multiBamSummary to calculate read coverage correlations, followed by plotPCA and plotFingerprint to assess enrichment and data quality. This Skill orchestrates these tools to generate comprehensive QC visualizations.
Yes, you can compare coverage tracks across multiple NGS samples directly from BAM files by using the bamCompare tool. This Skill enables comparative analysis by normalizing multiple samples and generating visualizations to assess relative enrichment.
Yes, this deepTools workflow supports ATAC-seq fingerprint plots for enrichment QC by utilizing the plotFingerprint tool. It assesses sample quality and enrichment levels to ensure your ATAC-seq data meets publication standards.
Use computeMatrix before plotting profiles around genomic features because it calculates and prepares the signal score matrix required by visualization tools. This Skill relies on computeMatrix output to generate accurate heatmaps and profile plots for publication-ready figures.
dralkhValidate and process sequencing coverage files for normalization, QC, and visualization.
jimmc414Convert BAM files to normalized bigWig coverage tracks.
zongtingweiProcess ATAC-seq data into QC metrics, peak calls, and accessible region summaries.
galeepAutomate NGS data processing and analysis with the deepTools suite.
