GENCODEHub provides stable AnnotationHub access to
annotation resources derived from GENCODE human release 50 for
GRCh38.p14 and Ensembl release 116. The collection is useful when an
analysis needs the original GTF attributes in feature-specific
GRanges objects or gene–transcript structure in a
TxDb. It complements general Ensembl and UCSC annotation
clients by distributing a fixed, documented GENCODE release with
persistent AnnotationHub identifiers.
The collection contains a GRanges with every imported
GTF row, separate GRanges objects for each GTF feature
type, and a TxDb database. The files are hosted in Zenodo record
21784647 and are downloaded only when selected through
AnnotationHub.
Install GENCODEHub from Bioconductor with the version of
R associated with the current Bioconductor release.
| Resource | AH ID | Contents | Class | Download |
|---|---|---|---|---|
annotation |
AH122277 |
every imported GTF row | GRanges |
34.8 MB |
gene |
AH122278 |
gene features and attributes | GRanges |
1.3 MB |
transcript |
AH122279 |
transcript data | GRanges |
8.5 MB |
exon |
AH122280 |
exon features and attributes | GRanges |
22.4 MB |
CDS |
AH122281 |
CDS features and phase | GRanges |
11.6 MB |
UTR |
AH122282 |
untranslated-region features | GRanges |
10.2 MB |
start_codon |
AH122283 |
start-codon features | GRanges |
4.2 MB |
stop_codon |
AH122284 |
stop-codon features | GRanges |
4.7 MB |
Selenocysteine |
AH122285 |
selenocysteine features | GRanges |
4 KB |
TxDb |
AH122286 |
gene/transcript/exon/CDS relations | TxDb |
344.2 MB |
The feature-specific GRanges resources retain the
original type and all metadata columns imported from the
GTF. The TxDb supports structural queries but does not
retain every GTF attribute.
Create one AnnotationHub connection and reuse it throughout the session. Subsetting a hub lists metadata; double-bracket extraction downloads and loads one selected resource.
library(AnnotationHub)
#> Loading required package: BiocGenerics
#> Loading required package: generics
#>
#> Attaching package: 'generics'
#> The following objects are masked from 'package:base':
#>
#> as.difftime, as.factor, as.ordered, intersect, is.element, setdiff,
#> setequal, union
#>
#> Attaching package: 'BiocGenerics'
#> The following objects are masked from 'package:stats':
#>
#> IQR, mad, sd, var, xtabs
#> The following object is masked from 'package:utils':
#>
#> data
#> The following objects are masked from 'package:base':
#>
#> anyDuplicated, aperm, append, as.data.frame, basename, cbind,
#> colnames, dirname, do.call, duplicated, eval, evalq, Filter, Find,
#> get, grep, grepl, is.unsorted, lapply, Map, mapply, match, mget,
#> order, paste, pmax, pmax.int, pmin, pmin.int, Position, rank,
#> rbind, Reduce, rownames, sapply, saveRDS, scale, sequence, table,
#> tapply, transform, unique, unsplit, which.max, which.min
#> Loading required package: BiocFileCache
#> Loading required package: dbplyr
library(GENCODEHub)
hub <- AnnotationHub(ask = FALSE)
resources <- gencodeV50Resources(hub)
resources
#> AnnotationHub with 10 records
#> # snapshotDate(): 2026-09-18
#> # $dataprovider: GENCODE
#> # $species: Homo sapiens
#> # $rdataclass: GRanges, TxDb
#> # additional mcols(): taxonomyid, genome, description,
#> # coordinate_1_based, maintainer, rdatadateadded, preparerclass, tags,
#> # rdatapath, sourceurl, sourcetype
#> # retrieve records with, e.g., 'object[["AH122277"]]'
#>
#> title
#> AH122277 | GENCODE v50 annotation: all GTF features (GRCh38.p14)
#> AH122278 | GENCODE v50 annotation: gene (GRCh38.p14)
#> AH122279 | GENCODE v50 annotation: transcript (GRCh38.p14)
#> AH122280 | GENCODE v50 annotation: exon (GRCh38.p14)
#> AH122281 | GENCODE v50 annotation: CDS (GRCh38.p14)
#> AH122282 | GENCODE v50 annotation: UTR (GRCh38.p14)
#> AH122283 | GENCODE v50 annotation: start_codon (GRCh38.p14)
#> AH122284 | GENCODE v50 annotation: stop_codon (GRCh38.p14)
#> AH122285 | GENCODE v50 annotation: Selenocysteine (GRCh38.p14)
#> AH122286 | GENCODE v50 annotation: TxDb (GRCh38.p14)gencodeResources() queries all records associated with
GENCODEHub, while gencodeV50Resources()
returns the ten release 50 records in AH-ID order. Detailed production
status and file sizes are available without downloading the resource
files.
getInfoOnIds(hub, names(resources))
#> ah_id fetch_id title
#> 346049 AH122277 129023 GENCODE v50 annotation: all GTF features (GRCh38.p14)
#> 346050 AH122278 129024 GENCODE v50 annotation: gene (GRCh38.p14)
#> 346051 AH122279 129025 GENCODE v50 annotation: transcript (GRCh38.p14)
#> 346052 AH122280 129026 GENCODE v50 annotation: exon (GRCh38.p14)
#> 346053 AH122281 129027 GENCODE v50 annotation: CDS (GRCh38.p14)
#> 346054 AH122282 129028 GENCODE v50 annotation: UTR (GRCh38.p14)
#> 346055 AH122283 129029 GENCODE v50 annotation: start_codon (GRCh38.p14)
#> 346056 AH122284 129030 GENCODE v50 annotation: stop_codon (GRCh38.p14)
#> 346057 AH122285 129031 GENCODE v50 annotation: Selenocysteine (GRCh38.p14)
#> 346058 AH122286 129032 GENCODE v50 annotation: TxDb (GRCh38.p14)
#> rdataclass status biocversion rdatadateadded rdatadateremoved file_size
#> 346049 GRanges Public 3.24 2026-08-06 <NA> 34815684
#> 346050 GRanges Public 3.24 2026-08-06 <NA> 1292008
#> 346051 GRanges Public 3.24 2026-08-06 <NA> 8532344
#> 346052 GRanges Public 3.24 2026-08-06 <NA> 22437820
#> 346053 GRanges Public 3.24 2026-08-06 <NA> 11642732
#> 346054 GRanges Public 3.24 2026-08-06 <NA> 10171044
#> 346055 GRanges Public 3.24 2026-08-06 <NA> 4203232
#> 346056 GRanges Public 3.24 2026-08-06 <NA> 4653192
#> 346057 GRanges Public 3.24 2026-08-06 <NA> 4064
#> 346058 TxDb Public 3.24 2026-08-06 <NA> 344219648The standard AnnotationHub interface and the package helper are equivalent. The small selenocysteine resource is used here so that the vignette exercises the production download and dispatch path without a large transfer.
selenocysteine <- hub[["AH122285"]]
#> downloading 1 resources
#> retrieving 1 resource
#> loading from cache
#> require("GenomicRanges")
selenocysteine_from_helper <- gencodeV50("Selenocysteine", hub)
#> loading from cache
stopifnot(identical(selenocysteine, selenocysteine_from_helper))
selenocysteine
#> GRanges object with 155 ranges and 22 metadata columns:
#> seqnames ranges strand | source type score
#> <Rle> <IRanges> <Rle> | <factor> <factor> <numeric>
#> [1] chr1 25802093-25802095 + | HAVANA Selenocysteine NA
#> [2] chr1 25812789-25812791 + | HAVANA Selenocysteine NA
#> [3] chr1 25812789-25812791 + | HAVANA Selenocysteine NA
#> [4] chr1 25812789-25812791 + | HAVANA Selenocysteine NA
#> [5] chr1 25812789-25812791 + | HAVANA Selenocysteine NA
#> ... ... ... ... . ... ... ...
#> [151] chr22 31105951-31105953 - | HAVANA Selenocysteine NA
#> [152] chr22 31105951-31105953 - | HAVANA Selenocysteine NA
#> [153] chr22 31105951-31105953 - | HAVANA Selenocysteine NA
#> [154] chr22 50217358-50217360 + | HAVANA Selenocysteine NA
#> [155] chr22 50217358-50217360 + | HAVANA Selenocysteine NA
#> phase gene_id gene_type gene_name level
#> <integer> <character> <character> <character> <character>
#> [1] <NA> ENSG00000162430.19 protein_coding SELENON 2
#> [2] <NA> ENSG00000162430.19 protein_coding SELENON 2
#> [3] <NA> ENSG00000162430.19 protein_coding SELENON 2
#> [4] <NA> ENSG00000162430.19 protein_coding SELENON 2
#> [5] <NA> ENSG00000162430.19 protein_coding SELENON 2
#> ... ... ... ... ... ...
#> [151] <NA> ENSG00000198832.12 protein_coding SELENOM 2
#> [152] <NA> ENSG00000198832.12 protein_coding SELENOM 2
#> [153] <NA> ENSG00000198832.12 protein_coding SELENOM 2
#> [154] <NA> ENSG00000073169.16 protein_coding SELENOO 2
#> [155] <NA> ENSG00000073169.16 protein_coding SELENOO 2
#> tag transcript_id transcript_type transcript_name
#> <character> <character> <character> <character>
#> [1] seleno ENST00000361547.8 protein_coding SELENON-202
#> [2] seleno ENST00000361547.8 protein_coding SELENON-202
#> [3] seleno ENST00001144438.1 protein_coding SELENON-205
#> [4] seleno ENST00000374315.1 protein_coding SELENON-203
#> [5] seleno ENST00000354177.9 protein_coding SELENON-201
#> ... ... ... ... ...
#> [151] seleno ENST00001134254.1 protein_coding SELENOM-210
#> [152] seleno ENST00000402395.5 protein_coding SELENOM-202
#> [153] seleno ENST00000400299.6 protein_coding SELENOM-201
#> [154] seleno ENST00001133157.1 protein_coding SELENOO-203
#> [155] seleno ENST00000380903.7 protein_coding SELENOO-201
#> exon_number exon_id transcript_support_level havana_transcript
#> <character> <character> <character> <character>
#> [1] <NA> <NA> 1 OTTHUMT00000019314.3
#> [2] <NA> <NA> 1 OTTHUMT00000019314.3
#> [3] <NA> <NA> <NA> <NA>
#> [4] <NA> <NA> 5 OTTHUMT00000019315.2
#> [5] <NA> <NA> 5 <NA>
#> ... ... ... ... ...
#> [151] <NA> <NA> <NA> <NA>
#> [152] <NA> <NA> 1 OTTHUMT00000321789.1
#> [153] <NA> <NA> 1 OTTHUMT00000321788.1
#> [154] <NA> <NA> <NA> <NA>
#> [155] <NA> <NA> 1 OTTHUMT00000075003.3
#> hgnc_id havana_gene ont protein_id
#> <character> <character> <character> <character>
#> [1] HGNC:15999 OTTHUMG00000007375.5 <NA> ENSP00000355141.2
#> [2] HGNC:15999 OTTHUMG00000007375.5 <NA> ENSP00000355141.2
#> [3] HGNC:15999 OTTHUMG00000007375.5 <NA> ENSP00000810384.1
#> [4] HGNC:15999 OTTHUMG00000007375.5 <NA> ENSP00000363434.1
#> [5] HGNC:15999 OTTHUMG00000007375.5 <NA> ENSP00000346109.5
#> ... ... ... ... ...
#> [151] HGNC:30397 OTTHUMG00000151207.1 <NA> ENSP00000812162.1
#> [152] HGNC:30397 OTTHUMG00000151207.1 <NA> ENSP00000384564.1
#> [153] HGNC:30397 OTTHUMG00000151207.1 <NA> ENSP00000383155.2
#> [154] HGNC:30395 OTTHUMG00000044645.4 <NA> ENSP00000811180.1
#> [155] HGNC:30395 OTTHUMG00000044645.4 <NA> ENSP00000370288.2
#> ccdsid artif_dupl
#> <character> <character>
#> [1] CCDS41282.1 <NA>
#> [2] CCDS41282.1 <NA>
#> [3] CCDS41283.1 <NA>
#> [4] CCDS41283.1 <NA>
#> [5] <NA> <NA>
#> ... ... ...
#> [151] CCDS43003.1 <NA>
#> [152] CCDS43003.1 <NA>
#> [153] CCDS43003.1 <NA>
#> [154] CCDS43034.1 <NA>
#> [155] CCDS43034.1 <NA>
#> -------
#> seqinfo: 25 sequences from GRCh38 genome; no seqlengthsThe gene resource is suitable for gene-body overlap and gene-level transcription start site annotation.
genes <- gencodeV50("gene", hub)
#> downloading 1 resources
#> retrieving 1 resource
#> loading from cache
genes
#> GRanges object with 78733 ranges and 22 metadata columns:
#> seqnames ranges strand | source type score phase
#> <Rle> <IRanges> <Rle> | <factor> <factor> <numeric> <integer>
#> [1] chr1 11121-24894 + | HAVANA gene NA <NA>
#> [2] chr1 12010-13670 + | HAVANA gene NA <NA>
#> [3] chr1 14356-30744 - | HAVANA gene NA <NA>
#> [4] chr1 14696-24886 - | HAVANA gene NA <NA>
#> [5] chr1 17369-17436 - | ENSEMBL gene NA <NA>
#> ... ... ... ... . ... ... ... ...
#> [78729] chrM 14149-14673 - | ENSEMBL gene NA <NA>
#> [78730] chrM 14674-14742 - | ENSEMBL gene NA <NA>
#> [78731] chrM 14747-15887 + | ENSEMBL gene NA <NA>
#> [78732] chrM 15888-15953 + | ENSEMBL gene NA <NA>
#> [78733] chrM 15956-16023 - | ENSEMBL gene NA <NA>
#> gene_id gene_type gene_name level
#> <character> <character> <character> <character>
#> [1] ENSG00000290825.2 lncRNA DDX11L16 2
#> [2] ENSG00000223972.6 transcribed_unproces.. DDX11L1 2
#> [3] ENSG00000310526.1 lncRNA WASH7P 2
#> [4] ENSG00000227232.6 transcribed_unproces.. WASH7P 2
#> [5] ENSG00000278267.1 miRNA MIR6859-1 3
#> ... ... ... ... ...
#> [78729] ENSG00000198695.2 protein_coding MT-ND6 3
#> [78730] ENSG00000210194.1 Mt_tRNA MT-TE 3
#> [78731] ENSG00000198727.2 protein_coding MT-CYB 3
#> [78732] ENSG00000210195.2 Mt_tRNA MT-TT 3
#> [78733] ENSG00000210196.2 Mt_tRNA MT-TP 3
#> tag transcript_id transcript_type transcript_name
#> <character> <character> <character> <character>
#> [1] overlaps_pseudogene <NA> <NA> <NA>
#> [2] <NA> <NA> <NA> <NA>
#> [3] overlaps_pseudogene <NA> <NA> <NA>
#> [4] overlapping_locus <NA> <NA> <NA>
#> [5] <NA> <NA> <NA> <NA>
#> ... ... ... ... ...
#> [78729] <NA> <NA> <NA> <NA>
#> [78730] <NA> <NA> <NA> <NA>
#> [78731] <NA> <NA> <NA> <NA>
#> [78732] <NA> <NA> <NA> <NA>
#> [78733] <NA> <NA> <NA> <NA>
#> exon_number exon_id transcript_support_level havana_transcript
#> <character> <character> <character> <character>
#> [1] <NA> <NA> <NA> <NA>
#> [2] <NA> <NA> <NA> <NA>
#> [3] <NA> <NA> <NA> <NA>
#> [4] <NA> <NA> <NA> <NA>
#> [5] <NA> <NA> <NA> <NA>
#> ... ... ... ... ...
#> [78729] <NA> <NA> <NA> <NA>
#> [78730] <NA> <NA> <NA> <NA>
#> [78731] <NA> <NA> <NA> <NA>
#> [78732] <NA> <NA> <NA> <NA>
#> [78733] <NA> <NA> <NA> <NA>
#> hgnc_id havana_gene ont protein_id ccdsid
#> <character> <character> <character> <character> <character>
#> [1] <NA> <NA> <NA> <NA> <NA>
#> [2] HGNC:37102 OTTHUMG00000000961.2 <NA> <NA> <NA>
#> [3] HGNC:38034 <NA> <NA> <NA> <NA>
#> [4] HGNC:38034 OTTHUMG00000000958.1 <NA> <NA> <NA>
#> [5] HGNC:50039 <NA> <NA> <NA> <NA>
#> ... ... ... ... ... ...
#> [78729] HGNC:7462 <NA> <NA> <NA> <NA>
#> [78730] HGNC:7479 <NA> <NA> <NA> <NA>
#> [78731] HGNC:7427 <NA> <NA> <NA> <NA>
#> [78732] HGNC:7499 <NA> <NA> <NA> <NA>
#> [78733] HGNC:7494 <NA> <NA> <NA> <NA>
#> artif_dupl
#> <character>
#> [1] <NA>
#> [2] <NA>
#> [3] <NA>
#> [4] <NA>
#> [5] <NA>
#> ... ...
#> [78729] <NA>
#> [78730] <NA>
#> [78731] <NA>
#> [78732] <NA>
#> [78733] <NA>
#> -------
#> seqinfo: 25 sequences from GRCh38 genome; no seqlengthsIdentifiers are retained as supplied by GENCODE, including version suffixes.
head(S4Vectors::mcols(genes)[, c("gene_id", "gene_name", "gene_type")])
#> DataFrame with 6 rows and 3 columns
#> gene_id gene_name gene_type
#> <character> <character> <character>
#> 1 ENSG00000290825.2 DDX11L16 lncRNA
#> 2 ENSG00000223972.6 DDX11L1 transcribed_unproces..
#> 3 ENSG00000310526.1 WASH7P lncRNA
#> 4 ENSG00000227232.6 WASH7P transcribed_unproces..
#> 5 ENSG00000278267.1 MIR6859-1 miRNA
#> 6 ENSG00000243485.6 MIR1302-2HG lncRNA
GenomeInfoDb::seqinfo(genes)
#> Seqinfo object with 25 sequences from GRCh38 genome; no seqlengths:
#> seqnames seqnames seqlengths isCircular genome
#> 1 chr1 <NA> <NA> GRCh38
#> 2 chr2 <NA> <NA> GRCh38
#> 3 chr3 <NA> <NA> GRCh38
#> 4 chr4 <NA> <NA> GRCh38
#> 5 chr5 <NA> <NA> GRCh38
#> ... ... ... ... ...
#> 21 chr21 <NA> <NA> GRCh38
#> 22 chr22 <NA> <NA> GRCh38
#> 23 chrX <NA> <NA> GRCh38
#> 24 chrY <NA> <NA> GRCh38
#> 25 chrM <NA> <NA> GRCh38The ranges use one-based, closed coordinates and GENCODE chromosome
names (chr1 through chr22, chrX,
chrY, and chrM). The genome identifier is
GRCh38; the assembly provenance GRCh38.p14 is
recorded in the objects and AnnotationHub metadata. The source GTF does
not provide chromosome lengths, so seqlengths() are
NA. The imported GRanges objects do not set
chrM circularity; the TxDb records
chrM as circular.
Gene and transcript resources contain the original source ranges. A strand-aware, one-base transcription start site can be derived without fixing a promoter width in the distributed annotation.
gene_tss <- GenomicRanges::resize(
genes,
width = 1L,
fix = "start"
)
gene_tss
#> GRanges object with 78733 ranges and 22 metadata columns:
#> seqnames ranges strand | source type score phase
#> <Rle> <IRanges> <Rle> | <factor> <factor> <numeric> <integer>
#> [1] chr1 11121 + | HAVANA gene NA <NA>
#> [2] chr1 12010 + | HAVANA gene NA <NA>
#> [3] chr1 30744 - | HAVANA gene NA <NA>
#> [4] chr1 24886 - | HAVANA gene NA <NA>
#> [5] chr1 17436 - | ENSEMBL gene NA <NA>
#> ... ... ... ... . ... ... ... ...
#> [78729] chrM 14673 - | ENSEMBL gene NA <NA>
#> [78730] chrM 14742 - | ENSEMBL gene NA <NA>
#> [78731] chrM 14747 + | ENSEMBL gene NA <NA>
#> [78732] chrM 15888 + | ENSEMBL gene NA <NA>
#> [78733] chrM 16023 - | ENSEMBL gene NA <NA>
#> gene_id gene_type gene_name level
#> <character> <character> <character> <character>
#> [1] ENSG00000290825.2 lncRNA DDX11L16 2
#> [2] ENSG00000223972.6 transcribed_unproces.. DDX11L1 2
#> [3] ENSG00000310526.1 lncRNA WASH7P 2
#> [4] ENSG00000227232.6 transcribed_unproces.. WASH7P 2
#> [5] ENSG00000278267.1 miRNA MIR6859-1 3
#> ... ... ... ... ...
#> [78729] ENSG00000198695.2 protein_coding MT-ND6 3
#> [78730] ENSG00000210194.1 Mt_tRNA MT-TE 3
#> [78731] ENSG00000198727.2 protein_coding MT-CYB 3
#> [78732] ENSG00000210195.2 Mt_tRNA MT-TT 3
#> [78733] ENSG00000210196.2 Mt_tRNA MT-TP 3
#> tag transcript_id transcript_type transcript_name
#> <character> <character> <character> <character>
#> [1] overlaps_pseudogene <NA> <NA> <NA>
#> [2] <NA> <NA> <NA> <NA>
#> [3] overlaps_pseudogene <NA> <NA> <NA>
#> [4] overlapping_locus <NA> <NA> <NA>
#> [5] <NA> <NA> <NA> <NA>
#> ... ... ... ... ...
#> [78729] <NA> <NA> <NA> <NA>
#> [78730] <NA> <NA> <NA> <NA>
#> [78731] <NA> <NA> <NA> <NA>
#> [78732] <NA> <NA> <NA> <NA>
#> [78733] <NA> <NA> <NA> <NA>
#> exon_number exon_id transcript_support_level havana_transcript
#> <character> <character> <character> <character>
#> [1] <NA> <NA> <NA> <NA>
#> [2] <NA> <NA> <NA> <NA>
#> [3] <NA> <NA> <NA> <NA>
#> [4] <NA> <NA> <NA> <NA>
#> [5] <NA> <NA> <NA> <NA>
#> ... ... ... ... ...
#> [78729] <NA> <NA> <NA> <NA>
#> [78730] <NA> <NA> <NA> <NA>
#> [78731] <NA> <NA> <NA> <NA>
#> [78732] <NA> <NA> <NA> <NA>
#> [78733] <NA> <NA> <NA> <NA>
#> hgnc_id havana_gene ont protein_id ccdsid
#> <character> <character> <character> <character> <character>
#> [1] <NA> <NA> <NA> <NA> <NA>
#> [2] HGNC:37102 OTTHUMG00000000961.2 <NA> <NA> <NA>
#> [3] HGNC:38034 <NA> <NA> <NA> <NA>
#> [4] HGNC:38034 OTTHUMG00000000958.1 <NA> <NA> <NA>
#> [5] HGNC:50039 <NA> <NA> <NA> <NA>
#> ... ... ... ... ... ...
#> [78729] HGNC:7462 <NA> <NA> <NA> <NA>
#> [78730] HGNC:7479 <NA> <NA> <NA> <NA>
#> [78731] HGNC:7427 <NA> <NA> <NA> <NA>
#> [78732] HGNC:7499 <NA> <NA> <NA> <NA>
#> [78733] HGNC:7494 <NA> <NA> <NA> <NA>
#> artif_dupl
#> <character>
#> [1] <NA>
#> [2] <NA>
#> [3] <NA>
#> [4] <NA>
#> [5] <NA>
#> ... ...
#> [78729] <NA>
#> [78730] <NA>
#> [78731] <NA>
#> [78732] <NA>
#> [78733] <NA>
#> -------
#> seqinfo: 25 sequences from GRCh38 genome; no seqlengthsThe TxDb record is substantially larger than the feature-specific resources. Its metadata can be inspected without downloading the 344 MB SQLite file.
getInfoOnIds(hub, "AH122286")
#> ah_id fetch_id title rdataclass
#> 346058 AH122286 129032 GENCODE v50 annotation: TxDb (GRCh38.p14) TxDb
#> status biocversion rdatadateadded rdatadateremoved file_size
#> 346058 Public 3.24 2026-08-06 <NA> 344219648Load it when transcript, exon, and coding-sequence relationships are required. This deliberately unevaluated example avoids downloading the large database during every vignette build; the evaluated examples above exercise the same AnnotationHub download and cache mechanism.
The resources were generated from the official GENCODE release 50 comprehensive gene annotation on the reference chromosomes:
https://ftp.ebi.ac.uk/pub/databases/gencode/Gencode_human/
release_50/gencode.v50.annotation.gtf.gzThe source checksum, transformation procedure, resource counts, build
session, and resource checksums are recorded in the Zenodo deposit and
in inst/scripts/make-data.R. For reproducible analyses,
record the GENCODE release, genome assembly, AH ID,
snapshotDate(hub), package version, and Zenodo DOI. Cite
the applicable publication listed on the GENCODE
project website, the Zenodo record, and GENCODEHub.
sessionInfo()
#> R version 4.6.1 (2026-06-24)
#> Platform: x86_64-pc-linux-gnu
#> Running under: Ubuntu 26.04.1 LTS
#>
#> Matrix products: default
#> BLAS: /usr/lib/x86_64-linux-gnu/openblas-pthread/libblas.so.3
#> LAPACK: /usr/lib/x86_64-linux-gnu/openblas-pthread/libopenblasp-r0.3.32.so; LAPACK version 3.12.0
#>
#> locale:
#> [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C
#> [3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8
#> [5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8
#> [7] LC_PAPER=en_US.UTF-8 LC_NAME=C
#> [9] LC_ADDRESS=C LC_TELEPHONE=C
#> [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
#>
#> time zone: Etc/UTC
#> tzcode source: system (glibc)
#>
#> attached base packages:
#> [1] stats4 stats graphics grDevices utils datasets methods
#> [8] base
#>
#> other attached packages:
#> [1] GenomicRanges_1.65.4 Seqinfo_1.3.2 IRanges_2.47.5
#> [4] S4Vectors_0.51.10 GENCODEHub_0.99.0 AnnotationHub_4.3.2
#> [7] BiocFileCache_3.3.0 dbplyr_2.6.0 BiocGenerics_0.59.12
#> [10] generics_0.1.4 BiocStyle_2.41.0
#>
#> loaded via a namespace (and not attached):
#> [1] KEGGREST_1.53.6 rjson_0.2.23 xfun_0.61
#> [4] bslib_0.12.0 httr2_1.3.0 lattice_0.23-1
#> [7] Biobase_2.73.2 vctrs_0.7.3 tools_4.6.1
#> [10] bitops_1.1-0 parallel_4.6.1 curl_8.0.0
#> [13] tibble_3.3.1 AnnotationDbi_1.75.2 RSQLite_3.53.3
#> [16] blob_1.3.0 pkgconfig_2.0.3 BiocBaseUtils_1.15.1
#> [19] Matrix_1.7-6 cigarillo_1.3.1 lifecycle_1.0.5
#> [22] compiler_4.6.1 Rsamtools_2.29.0 Biostrings_2.81.9
#> [25] codetools_0.2-20 GenomeInfoDb_1.49.1 htmltools_0.5.9
#> [28] sys_3.4.3 buildtools_1.0.0 sass_0.4.10
#> [31] RCurl_1.98-1.20 yaml_2.3.12 pillar_1.11.1
#> [34] crayon_1.5.3 jquerylib_0.1.4 BiocParallel_1.47.0
#> [37] cachem_1.1.0 tidyselect_1.2.1 digest_0.6.39
#> [40] purrr_1.2.2 dplyr_1.2.1 restfulr_0.0.17
#> [43] BiocVersion_3.24.0 maketools_1.3.2 grid_4.6.1
#> [46] fastmap_1.2.0 cli_3.6.6 magrittr_2.0.5
#> [49] GenomicFeatures_1.65.0 XML_3.99-0.25 withr_3.0.3
#> [52] UCSC.utils_1.9.0 filelock_1.0.3 rappdirs_0.3.4
#> [55] bit64_4.8.6 rmarkdown_2.32 XVector_0.53.0
#> [58] httr_1.4.9 bit_4.6.0 otel_0.2.0
#> [61] png_0.1-9 memoise_2.0.1 evaluate_1.0.5
#> [64] knitr_1.52 BiocIO_1.23.3 rtracklayer_1.73.0
#> [67] rlang_1.3.0 glue_1.8.1 DBI_1.3.0
#> [70] BiocManager_1.30.27 jsonlite_2.0.0 R6_2.6.1
#> [73] GenomicAlignments_1.49.2