Package: TxParq.Hs.gencode.v49 0.99.2

Vince Carey

TxParq.Hs.gencode.v49: Parquet-based representation of GENCODE gene models v49 for Homo sapiens

This is a parquet-based representation of GENCODE gene models v49 for Homo sapiens. Parquet is chosen to reduce footprint, to support tidyverse-oriented operations natively, and to provide opportunities for cloud-backed annotation services. Community contributions to functionality and architecture are welcome.

Authors:Vince Carey [aut, cre]

TxParq.Hs.gencode.v49_0.99.2.tar.gz
TxParq.Hs.gencode.v49_0.99.2.zip(r-4.7)TxParq.Hs.gencode.v49_0.99.2.zip(r-4.6)TxParq.Hs.gencode.v49_0.99.2.zip(r-4.5)
TxParq.Hs.gencode.v49_0.99.2.tgz(r-4.6-any)TxParq.Hs.gencode.v49_0.99.2.tgz(r-4.5-any)
TxParq.Hs.gencode.v49_0.99.2.tar.gz(r-4.7-any)TxParq.Hs.gencode.v49_0.99.2.tar.gz(r-4.6-any)
TxParq.Hs.gencode.v49_0.99.2.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
card.svg |card.png
TxParq.Hs.gencode.v49/json (API)

# Install 'TxParq.Hs.gencode.v49' in R:
install.packages('TxParq.Hs.gencode.v49', repos = c('https://biocstaging.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/vjcitn/txparq.hs.gencode.v49/issues

On CRAN:

Conda:

infrastructure

3.00 score 5 scripts 20 exports 79 dependencies

Last updated from:101fb29996. Checks:1 WARNING, 7 NOTE, 2 OK. Indexed: yes.

TargetResultTimeFilesSyslog
bioc-checksWARNING206
linux-devel-x86_64NOTE498
source / vignettesOK419
linux-release-x86_64NOTE472
macos-release-arm64NOTE378
macos-oldrel-arm64NOTE524
windows-develNOTE436
windows-releaseNOTE473
windows-oldrelNOTE456
wasm-releaseOK221

Exports:cdscdsBycodonsexonsexonsBygene_typesgenesgenes_in_regiongenomegtf_metadataGTFParquetlncRNA_genesprotein_coding_genesseqinfoshowtranscript_typestranscriptstranscripts_in_regiontranscriptsByutrs

Dependencies:abindAnnotationDbiarrowaskpassassertthatBHBiobaseBiocBaseUtilsBiocGenericsBiocIOBiocParallelBiostringsbitbit64bitopsblobcachemcigarilloclicodetoolscpp11crayoncurlDBIDelayedArraydplyrfastmapformatRfutile.loggerfutile.optionsgenericsGenomeInfoDbGenomicAlignmentsGenomicFeaturesGenomicRangesgluehttrIRangesjsonliteKEGGRESTlambda.rlatticelifecyclemagrittrMatrixMatrixGenericsmatrixStatsmemoisemimeopensslpillarpkgconfigpngpurrrR6RCurlrestfulrRhtslibrjsonrlangRsamtoolsRSQLitertracklayerS4ArraysS4VectorsSeqinfosnowSparseArraySummarizedExperimentsystibbletidyselectUCSC.utilsutf8vctrswithrXMLXVectoryaml

TxParq.Hs.gencode.v49: Parquet transformation of TxDb.Hs with Gencode v49

Vincent J. Carey, stvjc at channing.harvard.edu

Rendered fromTxParq.Hs.gencode.v49.Rmdusingknitr::rmarkdownon May 14 2026.

Last update: 2026-05-13
Started: 2026-05-12

Readme and manuals

Help Manual

Help pageTopics
List available gene or transcript typesbiotype-queries gene_types transcript_types
Convenience functions for common gene typesconvenience-functions lncRNA_genes protein_coding_genes
Extract genomic features from a GTFParquet objectcds,GTFParquet-method exons,GTFParquet-method genes genes,GTFParquet-method transcripts,GTFParquet-method
Get GTF metadatagtf_metadata
Create a GTFParquet objectGTFParquet
GTFParquet classgenome,GTFParquet-method GTFParquet-class seqinfo,GTFParquet-method
Find features overlapping a genomic regiongenes_in_region region-queries transcripts_in_region
printer for GTFParquetshow,GTFParquet-method
Extract and group genomic features from a GTFParquet objectcdsBy,GTFParquet-method exonsBy,GTFParquet-method transcriptsBy transcriptsBy,GTFParquet-method
Extract UTR and codon features from a GTFParquet objectcodons codons,GTFParquet-method utrs utrs,GTFParquet-method