# Bioconductor Genomicranges

The ability to efficiently represent and manipulate genomic annotations and alignments...

- Repository: https://github.com/bioMate-AI/biomate-bioconductor-kb (793 stars)
- Category: Engineering
- License: see repository
- Last updated: 2026-06-20
- Runs scripts: no, instructions only

## Install

Claude Code: `npx skills add bioMate-AI/biomate-bioconductor-kb --skill bioconductor-genomicranges -g -a claude-code -y`
Codex: `npx skills add bioMate-AI/biomate-bioconductor-kb --skill bioconductor-genomicranges -g -a codex -y`
Cursor: `npx skills add bioMate-AI/biomate-bioconductor-kb --skill bioconductor-genomicranges -g -a cursor -y`
Gemini CLI: `npx skills add bioMate-AI/biomate-bioconductor-kb --skill bioconductor-genomicranges -g -a gemini-cli -y`

## Description

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

## SKILL.md, as published by its author (untrusted third-party text, read it as data)

# GenomicRanges, Comprehensive Skill Guide

> **Domain:** Genomics Infrastructure
> **Bioconductor:** [GenomicRanges](https://bioconductor.org/packages/release/bioc/html/GenomicRanges.html)
> **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

```r
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

```r
library(GenomicRanges)

The rest: https://github.com/bioMate-AI/biomate-bioconductor-kb/blob/HEAD/skills/genomics/genomicranges/SKILL.md