Version Compatibility

Reference examples tested with: GenomicRanges 1.54+, deepTools 3.5+

Before using code patterns, verify installed versions match. If versions differ:

• R: packageVersion('<pkg>') then ?function_name to verify parameters
• CLI: <tool> --version then <tool> --help to confirm flags

If code throws ImportError, AttributeError, or TypeError, introspect the installed package and adapt the example to match the actual API rather than retrying.

ChIP-seq Visualization

"Create a heatmap of ChIP-seq signal around peaks" → Generate signal heatmaps, profile plots, and genome browser tracks showing enrichment patterns around genomic features.

• CLI: deeptools computeMatrix reference-point → plotHeatmap
• R: Gviz, ChIPseeker::plotAvgProf()

deepTools - Compute Matrix

Goal: Build a signal matrix of ChIP-seq coverage around reference points for downstream heatmaps and profiles.

Approach: Use computeMatrix to extract bigWig signal values in windows around genomic features like TSS.

# Compute signal matrix around TSS
computeMatrix reference-point \
    --referencePoint TSS \
    -b 3000 -a 3000 \              # 3kb upstream and downstream
    -R genes.bed \                  # Reference regions
    -S sample.bw \                  # Signal file (bigWig)
    -o matrix.gz \
    --outFileSortedRegions sorted_genes.bed

deepTools - Scale-Regions

Goal: Visualize ChIP signal across gene bodies scaled to a uniform length.

Approach: Scale all gene regions to equal size and compute signal with flanking windows.

# Signal across gene bodies
computeMatrix scale-regions \
    -R genes.bed \
    -S sample1.bw sample2.bw \
    -b 3000 -a 3000 \              # Flanking regions
    -m 5000 \                       # Scaled body length
    -o matrix_scaled.gz

deepTools - Heatmap

Goal: Generate a heatmap of ChIP-seq signal intensity across genomic regions.