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deeptools

combined

NGS analysis toolkit. BAM to bigWig conversion, QC (correlation, PCA, fingerprints), heatmaps/profiles (TSS, peaks), for ChIP-seq, RNA-seq, ATAC-seq visualization. NGS analysis toolkit. Used for BAM to bigWig conversion, quality control (correlation, PCA, fingerprint plots), heatmaps/feature plots (TSS, peaks), suitable for ChIP-seq, RNA-seq, ATAC-seq visualization.

When to use

• **File conversion**: "Convert BAM to bigWig", "generate coverage tracks", "normalize ChIP-seq data"
• **Quality control**: "check ChIP quality", "compare replicates", "assess sequencing depth", "QC analysis"
• **Visualization**: "create heatmap around TSS", "plot ChIP signal", "visualize enrichment", "generate profile plot"
• **Sample comparison**: "compare treatment vs control", "correlate samples", "PCA analysis"
• **Analysis workflows**: "analyze ChIP-seq data", "RNA-seq coverage", "ATAC-seq analysis", "complete workflow"
• **Working with specific file types**: BAM files, bigWig files, BED region files in genomics context
• Use this skill when you need ngs analysis toolkit. used for bam to bigwig conversion, quality control (correlation, pca, fingerprint plots), heatmaps/feature plots (tss, peaks), suitable for chip-seq, rna-seq, atac-seq visualization in a r…
• Use this skill when a data analytics task needs a packaged method instead of ad-hoc freeform output.

Skill page

Conflict

The K-Dense-AI copy is the most technically rigorous, containing specific 4.0.0 migration notes (Rust backend changes, removal of --ignoreDuplicates) and a detailed normalization guide. However, the FreedomIntelligence and aipoch copies contain specific workflow steps (ATAC-seq Tn5 offset correction, RNA-seq strand-specific filtering) and a general execution model that the K-Dense copy defers to external reference files. Because the K-Dense copy is truncated and relies on external references for the full workflow details that are explicitly present in the other copies, crowning it would hide the concrete procedural steps found in the others.