Bio Epitranscriptomics M6a Peak Calling
- 4 installs
- 1.1k repo stars
- Updated July 25, 2026
- gptomics/bioskills
Call m6A peaks from MeRIP-seq IP versus input comparisons using exomePeak2 to identify modification sites.
About
Identifies m6A modification sites by calling peaks from MeRIP-seq IP versus input samples with exomePeak2. A developer uses it when locating m6A sites from methylated RNA immunoprecipitation data.
- exomePeak2 IP-vs-input peak calling
- Identifies m6A modification sites
Bio Epitranscriptomics M6a Peak Calling by the numbers
- 4 all-time installs (skills.sh)
- Ranked #1,625 of 2,064 Data Science & ML skills by installs in the Skillselion catalog
- Data as of Aug 5, 2026 (Skillselion catalog sync)
npx skills add https://github.com/gptomics/bioskills --skill bio-epitranscriptomics-m6a-peak-callingAdd your badge
Show developers this skill is listed on Skillselion. Paste this into your README.
| Installs | 4 |
|---|---|
| repo stars | ★ 1.1k |
| Last updated | July 25, 2026 |
| Repository | gptomics/bioskills ↗ |
What it does
Call m6A peaks from MeRIP-seq IP versus input comparisons using exomePeak2 to identify modification sites.
Files
m6A Peak Calling
exomePeak2 (Recommended)
library(exomePeak2)
# Peak calling with biological replicates
result <- exomePeak2(
bam_ip = c('IP_rep1.bam', 'IP_rep2.bam'),
bam_input = c('Input_rep1.bam', 'Input_rep2.bam'),
gff = 'genes.gtf',
genome = 'hg38',
paired_end = TRUE
)
# Export peaks
exportResults(result, format = 'BED')MACS3 Alternative
# Call peaks treating input as control
macs3 callpeak \
-t IP_rep1.bam IP_rep2.bam \
-c Input_rep1.bam Input_rep2.bam \
-f BAMPE \
-g hs \
-n m6a_peaks \
--nomodel \
--extsize 150 \
-q 0.05MeTPeak
library(MeTPeak)
# GTF-aware peak calling
metpeak(
IP_BAM = c('IP_rep1.bam', 'IP_rep2.bam'),
INPUT_BAM = c('Input_rep1.bam', 'Input_rep2.bam'),
GENE_ANNO_GTF = 'genes.gtf',
OUTPUT_DIR = 'metpeak_output'
)Peak Filtering
# Filter by fold enrichment and q-value
# FC > 2, q < 0.05 typical thresholds
awk '$7 > 2 && $9 < 0.05' peaks.xls > filtered_peaks.bedRelated Skills
- merip-preprocessing - Prepare data for peak calling
- m6a-differential - Compare peaks between conditions
- chip-seq/peak-calling - Similar concepts
Related skills
Microsoft FoundryDeploy, evaluate, and continuously improve Microsoft Foundry agents from a single agent interface.490k1.3k
Ai Research ReproductionOrchestrate trustworthy, auditable reproduction of deep learning repositories directly from their READMEs.176k511Run TrainSafely execute selected deep learning training commands with standardized evidence capture.176k511Explore RunSafely run isolated exploratory experiments with clear recording and conservative selection before committing changes.176k511Paper Context ResolverFetch precise reproduction-critical details like dataset splits, preprocessing steps, or evaluation protocols from the original academic paper when the repo README leav141k511Repo Intake And PlanScan unfamiliar AI research repositories and receive a minimal, trustworthy reproduction target before investing significant time.140k511