Bioconductor Genomicranges
The ability to efficiently represent and manipulate genomic annotations and alignments...
Install
npx skills add bioMate-AI/biomate-bioconductor-kb --skill bioconductor-genomicranges -g -a claude-code -y- Repository
- bioMate-AI/biomate-bioconductor-kb793
- Category
- Engineering
- Updated
- 5mo ago
- License
- See repository
- Context cost
- Mediumabout 3,000 tokens
- Runs scripts
- No, instructions only
What it does
The ability to efficiently represent and manipulate genomic annotations and alignments is playing a central role when it comes to analyzing high-throughput sequencing data (a.k.a. NGS data). The GenomicRanges package defines general purpose
GenomicRanges, Comprehensive Skill Guide
Domain: Genomics Infrastructure Bioconductor: GenomicRanges Paper: Lawrence M et al. (2013). PLOS Computational Biology, 9:e1003118.
Infrastructure for representing and manipulating genomic intervals. The core workhorse for any genomic coordinate arithmetic in Bioconductor.
Dependencies & Environment
Package-intrinsic requirements from the Bioconductor landing page, reproduce in any R environment.
- Version: 1.64.0 · Bioconductor: 3.23 · R: ≥ 4.6
- Depends: BiocGenerics, S4Vectors, IRanges, Seqinfo
- Install:
BiocManager::install("GenomicRanges")
When to Use
- Overlap queries between genomic features
- Peak annotation and TSS proximity
- Windowed genome coverage computation
- Import/export BED/GFF/VCF/BigWig regions
- Tiling genome for ChIP-seq/ATAC-seq windows
Alternatives: IRanges (integer ranges only), plyranges (tidyverse-style)
Do NOT Use When
- Sequence manipulation (use Biostrings instead).
- Annotation retrieval (use AnnotationHub, biomaRt, or TxDb).
- Genome-wide statistics directly (use BSgenome or rtracklayer for coverage).
Data Requirements
| Requirement | Details |
|---|---|
| Input Format | BED, GFF/GTF (via rtracklayer), or programmatic construction from data frames |
Installation
if (!require("BiocManager", quietly=TRUE))
install.packages("BiocManager")
BiocManager::install("GenomicRanges")
library(GenomicRanges)
Workflows
Genomic interval manipulation and overlap analysis
Core operations: construct, manipulate, and intersect GRanges objects
Build and manipulate GRanges
library(GenomicRanges)
