# Bioconductor Genomicfeatures

> Extract the genomic locations of genes, transcripts, exons, introns, and CDS, for the gene models stored in a TxDb object. A TxDb object is a small database that contains the gene models of a given organism/assembly. Bioconductor provides a

- Skill: `biomate-ai/bioconductor-genomicfeatures` (Agent Skill)
- Install (CLI): `npx skillmds@latest add biomate-ai/bioconductor-genomicfeatures`
- Raw SKILL.md: https://api.skillmd.com/api/skills/biomate-ai/bioconductor-genomicfeatures/raw
- Safety review: pending
- Works with: Claude Code, Claude.ai, OpenAI Codex
- Category: Coding & Dev Tools
- Author: biomate-ai (https://skillmd.com/u/biomate-ai)
- Updated: 2026-09-17
- Page: https://skillmd.com/skills/biomate-ai/bioconductor-genomicfeatures

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# GenomicFeatures

## 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, GenomicRanges, AnnotationDbi
- **Imports:** DBI, XVector, Biostrings, rtracklayer
- **Install:** `BiocManager::install("GenomicFeatures")`

## When to Use
- Extract genomic coordinates for exons, transcripts, or coding sequences as `GRanges` objects using `transcripts`, `exons`, or `cds`.
- Group genomic features by gene or transcript into a `GRangesList` using `transcriptsBy` or `exonsBy`.
- Retrieve actual sequence data by pairing a `TxDb` with a `BSgenome` package and using `extractTranscriptSeqs`.

## When NOT to Use
- For extracting actual sequence data without a `BSgenome` package (use `BSgenome` directly instead because `GenomicFeatures` only stores coordinates).
- For finding overlaps between alignments and features without first extracting the features (use `findOverlaps` on the extracted `GRangesList` instead).

## Data Requirements
- Requires a `TxDb` object (loaded via `loadDb` or an annotation package like `TxDb.Hsapiens.UCSC.hg19.knownGene`).
- Sequence extraction requires an appropriate `BSgenome` package (e.g., `BSgenome.Hsapiens.UCSC.hg19`).

## Key Parameters
- **keys** (default): A vector of identifiers to look up when using `select`.
- **columns** (default): The columns to retrieve when using `select`.
- **keytype** (default): The type of key being passed to `select`.
- **filter** (default): A list (e.g., `tx_chrom`, `tx_strand`) to subset results in `transcripts`.
- **upstream** (default): Number of bases upstream from the transcription start site for `promoters`.
- **downstream** (default): Number of bases downstream from the transcription start site for `promoters`.
- **by** (default): The feature to group by (e.g., "gene", "tx") in `transcriptsBy` or `exonsBy`.
- **use.names** (default): Logical to retain sequence names in `extractTranscriptSeqs`.

## Best Practices
- Check active chromosomes using `seqlevels` before extracting features to limit the data returned.
- Use `select` to map between different identifiers (e.g., `TXNAME` to `GENEID`) within the `TxDb` object.
- Group features into a `GRangesList` (e.g., using `exonsBy`) before using `findOverlaps` to contextualize high-throughput sequencing alignments.

## Common Pitfalls
- Extracting sequences for all transcribed regions instead of just coding regions. Fix: Use `cdsBy` to subset coding regions before calling `extractTranscriptSeqs`.
- Translating non-coding sequences resulting in meaningless translations. Fix: Ensure you extract sequences using `cdsBy` before passing them to `translate`.
- Forgetting which chromosomes are active after filtering. Fix: Use `seqlevels0` to reset to the original chromosomes stored in the database.

## Alternatives
- `txdbmaker`: For making `TxDb` objects from genomic annotations (UCSC, Ensembl, GFF) rather than querying existing ones.
- `BSgenome`: For working directly with full genome sequences rather than transcript-specific metadata.
- `GenomicRanges`: For general manipulation of `GRanges` objects rather than extracting them from a database.

## Citations
- Carlson M, Aboyoun P, Pagès H, Falcon S, Morgan M (2026). "Obtaining and Utilizing TxDb Objects." Bioconductor Vignette.

## References
- Homepage: bioconductor.org/packages/GenomicFeatures
- Vignette: vignette_0_d47eae8b.txt

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## Run this on BioMate

This skill is the **knowledge layer** — when, why, and how to use `genomicfeatures`. To **run this analysis on your own data** with managed compute, automated QC, and reproducible outputs, use **[BioMate](https://www.biomate.ai?ref=kb&pkg=genomicfeatures)** — free to start.

▶ **[Open `genomicfeatures` on BioMate →](https://www.biomate.ai?ref=kb&pkg=genomicfeatures)**