Package 'GENCODEHub'

Title: GENCODE AnnotationHub
Description: Provides access through AnnotationHub to genomic annotation resources derived from GENCODE releases. The release 50 collection represents every feature type in the human GRCh38.p14 GTF. Feature-specific GRanges objects retain the imported identifiers and attributes, while a TxDb resource supports gene, transcript, exon, and coding-sequence queries.
Authors: Paul Ruiz Pinto [aut, cre] (ORCID: <https://orcid.org/0009-0007-6714-3566>)
Maintainer: Paul Ruiz Pinto <[email protected]>
License: Artistic-2.0
Version: 0.99.0
Built: 2026-10-07 11:58:24 UTC
Source: https://github.com/BiocStaging/GENCODEHub

Help Index

Discover GENCODE resources

Description

Discover GENCODE resources

Usage

gencodeResources(hub = AnnotationHub::AnnotationHub())

Arguments

hub

An AnnotationHub object. By default, a new hub connection is created with AnnotationHub::AnnotationHub(). Supplying an existing hub object avoids opening more than one connection in a session.

Details

Resource data are hosted remotely and cached by AnnotationHub after the first download. This function searches AnnotationHub metadata by the GENCODEHub package name and can therefore include resources added in later package releases.

Value

An AnnotationHub object restricted to GENCODEHub resources.

Examples

hub <- AnnotationHub::AnnotationHub(ask = FALSE)
gencodeResources(hub)

Retrieve a GENCODE v50 annotation resource

Description

Retrieve a GENCODE v50 annotation resource

Usage

gencodeV50(resource = "annotation", hub = AnnotationHub::AnnotationHub())

Arguments

resource

One resource name: "annotation", "gene", "transcript", "exon", "CDS", "UTR", "start_codon", "stop_codon", "Selenocysteine", or "TxDb".
hub

An AnnotationHub object. Supplying an existing hub object avoids opening more than one connection in a session.

Details

Gene- or transcript-level transcription start sites can be derived from the applicable GRanges resource with GenomicRanges::resize(x, width = 1L, fix = "start").

Retrieval uses the stable AnnotationHub identifier recorded for the selected resource. AnnotationHub downloads the file only on first use and then reuses its local cache.

Value

A GRanges object for GTF annotation resources or a TxDb object when resource = "TxDb".

Examples

hub <- AnnotationHub::AnnotationHub(ask = FALSE)
selenocysteine <- gencodeV50("Selenocysteine", hub)
selenocysteine

GENCODE release 50 AnnotationHub resources

Description

Ten annotation resources derived from the GENCODE release 50 GTF for the human GRCh38.p14 reference chromosomes. The collection contains nine GRanges resources and one TxDb resource.

Details

The annotation resource contains every imported GTF row. The gene, transcript, exon, CDS, UTR, start_codon, stop_codon, and Selenocysteine resources contain the corresponding original feature type. The TxDb resource stores gene, transcript, exon, and coding-sequence relationships.

The GRanges resources preserve versioned GENCODE identifiers and imported GTF attributes. Coordinates are one-based, closed intervals on GRCh38.p14. The TxDb is intended for structural queries and does not retain every GTF attribute. Sequence lengths are not present in the source GTF and are therefore NA. The TxDb records chrM as circular; the imported GRanges objects do not set circularity.

Value

The help topic documents a collection of GRanges and TxDb resources accessed through AnnotationHub.

AnnotationHub identifiers

annotation: AH122277; gene: AH122278; transcript: AH122279; exon: AH122280; CDS: AH122281; UTR: AH122282; start_codon: AH122283; stop_codon: AH122284; Selenocysteine: AH122285; and TxDb: AH122286.

Source

GENCODE Human Release 50, Ensembl release 116: https://www.gencodegenes.org/human/release_50.html.

The processed resources and checksums are deposited at doi:10.5281/zenodo.21784647.

Access

Use gencodeV50Resources() to list the resources and gencodeV50() to load one resource. The standard AnnotationHub interface can also be used directly, for example hub[["AH122278"]] for genes. AnnotationHub caches downloaded files for reuse.

Examples

hub <- AnnotationHub::AnnotationHub(ask = FALSE)
gencodeV50Resources(hub)
selenocysteine <- hub[["AH122285"]]
selenocysteine

Discover GENCODE v50 resources

Description

Discover GENCODE v50 resources

Usage

gencodeV50Resources(hub = AnnotationHub::AnnotationHub())

Arguments

hub

An AnnotationHub object. By default, a new hub connection is created with AnnotationHub::AnnotationHub(). Supplying an existing hub object avoids opening more than one connection in a session.

Details

The release 50 resources are selected by their stable AnnotationHub identifiers rather than by mutable titles.

Value

An AnnotationHub object restricted to the ten GENCODE release 50 resources, ordered from AH122277 through AH122286.

Examples

hub <- AnnotationHub::AnnotationHub(ask = FALSE)
gencodeV50Resources(hub)