Version Compatibility

Reference examples tested with: DESeq2 1.42+, HISAT2 2.2.1+, STAR 2.7.11+, Subread 2.0+, edgeR 4.0+, pandas 2.2+, scanpy 1.10+

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

• Python: pip show <package> then help(module.function) to check signatures
• 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.

featureCounts Counting

"Count reads per gene from my BAM files" → Assign aligned reads to genomic features using a GTF annotation to produce a gene-by-sample count matrix for DE analysis.

• CLI: featureCounts -a genes.gtf -o counts.txt sample1.bam sample2.bam

Count reads mapping to genomic features (genes, exons) from BAM files.