Version Compatibility

Reference examples tested with: bedtools 2.31+, matplotlib 3.8+, numpy 1.26+, pandas 2.2+, pyBigWig 0.3+, samtools 1.19+

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.

TF Footprinting

"Identify TF binding footprints in my ATAC-seq data" → Detect protected DNA regions within accessible chromatin where bound transcription factors block Tn5 insertion.

• CLI: TOBIAS ATACorrect → TOBIAS FootprintScores → TOBIAS BINDetect

TOBIAS Workflow