GENCODEHub

GENCODEHub is a Bioconductor AnnotationHub package for GENCODE human gene annotation. It provides GENCODE release 50 for GRCh38.p14 and Ensembl release 116 as separate GRanges resources and as a structural TxDb database.

The annotation files are hosted in Zenodo record 21784647. AnnotationHub downloads only the resource selected by the user and keeps a local cached copy for later use.

The release 50 collection has stable AnnotationHub identifiers AH122277 through AH122286.

1. Install the package

if (!requireNamespace("BiocManager", quietly = TRUE)) {
    install.packages("BiocManager")
}
BiocManager::install("GENCODEHub")

2. List the available resources

library(AnnotationHub)
library(GENCODEHub)

hub <- AnnotationHub()
gencodeV50Resources(hub)

The collection contains the complete GTF annotation, separate resources for gene, transcript, exon, CDS, UTR, start_codon, stop_codon, and Selenocysteine features, and a TxDb database.

Resource	AnnotationHub ID	Class
annotation	AH122277	GRanges
gene	AH122278	GRanges
transcript	AH122279	GRanges
exon	AH122280	GRanges
CDS	AH122281	GRanges
UTR	AH122282	GRanges
start_codon	AH122283	GRanges
stop_codon	AH122284	GRanges
Selenocysteine	AH122285	GRanges
TxDb	AH122286	TxDb

3. Retrieve the resource needed for an analysis

genes <- gencodeV50("gene", hub = hub)
transcripts <- gencodeV50("transcript", hub = hub)
txdb <- gencodeV50("TxDb", hub = hub)

The standard AnnotationHub interface can also be used directly:

genes <- hub[["AH122278"]]
resource_status <- getInfoOnIds(hub, "AH122278")

Use the gene resource for gene-body overlaps or gene-level transcription start sites. Use the transcript resource when transcript-specific coordinates are required. Use the TxDb for relationships among genes, transcripts, exons and coding sequences.

4. Check coordinates and identifiers

genes
head(genes$gene_id)
S4Vectors::mcols(genes)

The GRanges resources retain the versioned GENCODE identifiers and imported GTF attributes. Coordinates are one-based, closed intervals on GRCh38.p14. GRCh37 or hg19 data must be converted to GRCh38 before direct annotation. Chromosome lengths are not present in the source GTF and are therefore NA in the distributed sequence information. The TxDb records chrM as circular; the imported GRanges resources do not set circularity.

Source and citation

The resources are derived from GENCODE Human Release 50 using the official gencode.v50.annotation.gtf.gz file. Cite the applicable GENCODE publication, the Zenodo record and GENCODEHub when using the resources. Use citation("GENCODEHub") for the package citation.