Bio Epitranscriptomics M6a Differential

About this skill

Identifies differential m6A methylation between conditions from MeRIP-seq paired IP/input data using exomePeak2 with bamip + baminput (control arm) and bamtreatedip + bamtreatedinput (treatment arm) for integrated GC-bias-aware differential calling (Liu 2022 NAR Genom Bioinform 4:lqac046), QNB beta-binomial test (Liu 2017 BMC Bioinformatics 18:387), MeTDiff HMM-based differential bundled with MeTPeak, RADAR (Zhang 2019 Genome Biol 20:294) with its filterBins -> diffIP -> reportResult workflow, and the defensible paired-symmetric case of edgeR / DESeq2 on featureCounts-on-peaks matrices when batch / lot covariates need explicit fixed-effect handling (exomePeak2's top-level API does NOT accept arbitrary covariates).

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0 potential findings · Scanned 11/4/2026 · Scanner 0.2.1

Content SHA-256: a62302215f90569096b50a204a0bd3098f101b7d761fe78719b3b4e94c07c7eb

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Original listing metadata

Original name

bio-epitranscriptomics-m6a-differential

Original description

Identifies differential m6A methylation between conditions from MeRIP-seq paired IP/input data using exomePeak2 with `bam_ip` + `bam_input` (control arm) and `bam_treated_ip` + `bam_treated_input` (treatment arm) for integrated GC-bias-aware differential calling (Liu 2022 *NAR Genom Bioinform* 4:lqac046), QNB beta-binomial test (Liu 2017 *BMC Bioinformatics* 18:387), MeTDiff HMM-based differential bundled with MeTPeak, RADAR (Zhang 2019 *Genome Biol* 20:294) with its `filterBins -> diffIP -> reportResult` workflow, and the defensible paired-symmetric case of edgeR / DESeq2 on featureCounts-on-peaks matrices when batch / lot covariates need explicit fixed-effect handling (exomePeak2's top-level API does NOT accept arbitrary covariates).

About this listing

Category: Content & writing
Reported license: Not specified
Listing language (estimated): English
Review status: Not individually reviewed
Agent compatibility: Atlas installation supports Claude Code, Codex, and Cursor. Skill-specific dependencies and features are checked during setup.