Annotate ENCODE ChIP-seq and ATAC-seq peaks with genomic features.
npx skills add https://github.com/ammawla/encode-toolkit --skill peak-annotation
Please help me install this Agent Skill. Skill: peak-annotation Source: https://github.com/ammawla/encode-toolkit/tree/main/plugin/skills/peak-annotation Command: npx skills add https://github.com/ammawla/encode-toolkit --skill peak-annotation
This Skill helps researchers assign biological meaning to ENCODE peak datasets by annotating peaks with genomic features and functional annotations, facilitating downstream analysis.
Load your ENCODE peak file in BED format, annotate peaks with genomic features using ChIPseeker, and then perform GO enrichment on nearby genes with R packages.
High-intent search queries and answers about installing and using this skill.
To annotate ENCODE ChIP-seq peaks, load your BED format peak file and classify regions into promoter, intron, exon, and intergenic categories using the ChIPseeker R package for genomic feature annotation.
Functional enrichment analysis for genomic regions assigns biological meaning to peaks by performing gene ontology and pathway enrichment on peak-associated genes using tools like clusterProfiler and rGREAT.
Yes, you can use this workflow for ATAC-seq data, as the Skill explicitly supports annotating and interpreting genomic regions from both ENCODE ChIP-seq and ATAC-seq datasets.
Yes, you need R and Bioconductor packages like ChIPseeker, clusterProfiler, rGREAT, TxDb.Hsapiens.UCSC.hg38.knownGene, and org.Hs.eg.db to perform peak annotation and functional enrichment.
The best way to identify enriched biological processes from H3K27ac peaks is to annotate genomic features with ChIPseeker, then perform GO enrichment on nearby genes using clusterProfiler.
MDheweiAnnotate ATAC-seq or ChIP-seq peaks with genomic context and QC metrics.
TianGzlabPerform ATAC-seq and ChIP-seq peak calling with MACS3 and motif enrichment using Homer.
ya-wayAnalyzes Reactome pathway enrichment for gene lists using enrichPathway and gsePathway.
superfhpAccess bioinformatics skills for genomic, transcriptomic, and metagenomic analysis.
