Bioconductor Chipseeker
ChIPseeker is a Bioconductor package for annotating ChIP-seq data analysis.
Install
npx skills add bioMate-AI/biomate-bioconductor-kb --skill bioconductor-chipseeker -g -a claude-code -y- Repository
- bioMate-AI/biomate-bioconductor-kb793
- Category
- Data and ML
- Updated
- 5mo ago
- License
- See repository
- Context cost
- Mediumabout 3,000 tokens
- Runs scripts
- No, instructions only
What it does
ChIPseeker is a Bioconductor package for annotating ChIP-seq data analysis. Peak Annotation is performed by the annotatePeak function. The position and strand information of nearest genes are reported, in addition to the distance from the p
ChIPseeker, Comprehensive Skill Guide
Domain: ChIP-seq / ATAC-seq Bioconductor: ChIPseeker Paper: Yu G, Wang LG, He QY (2015). Bioinformatics, 31(14):2382-2383.
ChIP-seq peak annotation, comparison, and visualization. Annotates peaks to nearest genomic features, generates coverage and TSS profile plots.
Dependencies & Environment
Package-intrinsic requirements from the Bioconductor landing page, reproduce in any R environment.
- Version: 1.48.0 · Bioconductor: 3.23 · R: ≥ 4.6
- Imports: AnnotationDbi, aplot, BiocGenerics, boot, dplyr, enrichplot, IRanges, GenomeInfoDb, GenomicRanges, GenomicFeatures, ggplot2, gplots, gtools, magrittr, plotrix, RColorBrewer, rlang, rtracklayer, S4Vectors, scales, tibble, TxDb.Hsapiens.UCSC.hg19.knownGene, yulab.utils
- Install:
BiocManager::install("ChIPseeker")
When to Use
- Annotate ChIP-seq/ATAC-seq peaks to promoters, exons, introns, intergenic regions
- Profile read coverage around TSS (transcription start sites)
- Compare peak sets across experiments
- Functional enrichment of annotated peaks
Alternatives: HOMER annotatePeaks.pl, GREAT (web tool), GenomicFeatures
Do NOT Use When
- Differential binding analysis (use DiffBind or csaw).
- Motif analysis (use MEME-ChIP, HOMER, or universalmotif).
- De novo peak calling, peaks must already be called (MACS2, HOMER, etc.).
Data Requirements
| Requirement | Details |
|---|---|
| Input Format | BED/narrowPeak files, or GRanges objects of called peaks |
| Annotation Db | TxDb (e.g. TxDb.Hsapiens.UCSC.hg38.knownGene) + OrgDb (org.Hs.eg.db) |
| Genome Match | Peak genome assembly must match TxDb genome assembly exactly |
Installation
if (!require("BiocManager", quietly=TRUE))
install.packages("BiocManager")
BiocManager::install("ChIPseeker")
library(ChIPseeker)
