bio-epitranscriptomics-m6a-peak-calling

npx skills add BioTender-max/awesome-bio-agent-skills --skill m6a-peak-calling --agent claude-code

Same command for any agent — swap --agent for codex, cursor, copilot.

## Version Compatibility Reference examples tested with: MACS3 3.0+ 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. # m6A Peak Calling **"Call m6A peaks from my MeRIP-seq data"** → Identify m6A-modified RNA regions by comparing immunoprecipitated (IP) and input samples using statistical enrichment testing. - R: `exomePeak2::exomePeak2()` for GC-bias aware peak calling - CLI: `macs3 callpeak` as an alternative broad peak caller ## exomePeak2 (Recommended) **Goal:** Identify m6A-enriched regions by comparing IP and input samples with GC-bias correction and replicate-aware statistical testing. **Approach:** Provide IP and input BAM files along with a gene annotation to exomePeak2, which models read counts in sliding windows across the transcriptome and calls significant enrichment peaks. ```r library(exomePeak2) # Peak calling with biological replicates result

Call peaks treating input as control
macs3 callpeak \
Filter by fold enrichment and q-value
FC > 2, q < 0.05 typical thresholds
awk '$7 > 2 && $9 < 0.05' peaks.xls > filtered_peaks.bed