Version Compatibility

Reference examples tested with: pyGenomeTracks 3.9+, Gviz 1.46+ (Bioconductor), deepTools 3.5+, GenomicRanges 1.54+, IGV 2.18+ (batch mode).

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

• Python: pip show <package> then help(module.function)
• R: packageVersion('<pkg>') then ?function_name
• CLI: <tool> --version then <tool> --help

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

Genome Browser Tracks

"Plot a genomic locus with multiple tracks" -> Build a stacked figure where each track (coverage from BigWig, peaks from BED, genes from GTF, Hi-C from cool, loops from BedPE) is aligned to genome coordinates. The decisions that matter: track normalization (especially for ChIP-Rx spike-in), gene-model rendering style (UCSC vs FlyBase), y-axis sharing across samples, and which tool fits the workflow — pyGenomeTracks (config-driven, reproducible, headless), Gviz (R Bioconductor), IGV batch (interactive-tool screenshots).

• Python / CLI: pyGenomeTracks (Lopez-Delisle 2021 Bioinformatics 37:422)
• R: Gviz::plotTracks (Hahne-Ivanek 2016)
• Interactive: IGV (Robinson 2011 Nat Biotechnol 29:24) with batch scripting