Version Compatibility

Reference examples tested with: DESeq2 1.42+, MACS3 3.0+, STAR 2.7.11+, bedtools 2.31+, fastp 0.23+, samtools 1.19+

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.

MeRIP-seq Pipeline

"Analyze my MeRIP-seq data from FASTQ to differential m6A peaks" → Orchestrate read alignment (STAR), m6A peak calling (exomePeak2/MACS3), differential modification testing, and metagene/Guitar visualization of modification sites.

Pipeline Overview