Package: tximeta 1.31.4

Michael Love

tximeta: Transcript Quantification Import with Automatic Metadata

Transcript quantification import from Salmon and other quantifiers with automatic attachment of transcript ranges and release information, and other associated metadata. De novo transcriptomes can be linked to the appropriate sources with linkedTxomes and shared for computational reproducibility.

Authors:Michael Love [aut, cre], Charlotte Soneson [aut, ctb], Peter Hickey [aut, ctb], Rob Patro [aut, ctb], NIH NHGRI [fnd], CZI [fnd]

tximeta_1.31.4.tar.gz
tximeta_1.31.4.zip(r-4.7)tximeta_1.31.4.zip(r-4.6)tximeta_1.31.4.zip(r-4.5)
tximeta_1.31.4.tgz(r-4.6-any)tximeta_1.31.4.tgz(r-4.5-any)
tximeta_1.31.4.tar.gz(r-4.7-any)tximeta_1.31.4.tar.gz(r-4.6-any)
tximeta_1.31.4.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
tximeta/json (API)

# Install 'tximeta' in R:

install.packages('tximeta', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/thelovelab/tximeta/issues

Pkgdown/docs site:https://thelovelab.github.io

On BioConductor:tximeta-1.31.2(bioc 3.24)tximeta-1.30.0(bioc 3.23)

annotation genomeannotation dataimport preprocessing rnaseq longread singlecell transcriptomics transcription geneexpression functionalgenomics reproducibleresearch reportwriting immunooncology

10.96 score 72 stars 1 packages 668 scripts 11 mentions 17 exports 99 dependencies

Last updated from:6825c7f4a6. Checks:1 ERROR, 7 NOTE, 2 OK. Indexed: yes.

Target	Result	Time
bioc-checks	ERROR	276
linux-devel-x86_64	NOTE	630
source / vignettes	OK	544
linux-release-x86_64	NOTE	639
macos-release-arm64	NOTE	394
macos-oldrel-arm64	NOTE	384
windows-devel	NOTE	605
windows-release	NOTE	573
windows-oldrel	NOTE	606
wasm-release	OK	217

Exports:addCDS addExons addIds getTximetaBFC importData inspectDigests loadLinkedTxome makeDGEList makeLinkedTxome makeLinkedTxpData retrieveCDNA retrieveDb setTximetaBFC splitSE summarizeToGene tximeta updateMetadata

Dependencies:abind AnnotationDbi AnnotationFilter AnnotationHub askpass BH Biobase BiocBaseUtils BiocFileCache BiocGenerics BiocIO BiocManager BiocParallel BiocVersion biomaRt Biostrings bit bit64 bitops blob cachem cigarillo cli codetools cpp11 crayon curl DBI dbplyr DelayedArray dplyr ensembldb fastmap filelock formatR futile.logger futile.options generics GenomeInfoDb GenomicAlignments GenomicFeatures GenomicRanges glue hms httr httr2 IRanges jsonlite KEGGREST lambda.r lattice lazyeval lifecycle magrittr Matrix MatrixGenerics matrixStats memoise mime openssl pillar pkgconfig png prettyunits progress ProtGenerics purrr R6 rappdirs RCurl restfulr Rhtslib rjson rlang Rsamtools RSQLite rtracklayer S4Arrays S4Vectors Seqinfo snow SparseArray stringi stringr SummarizedExperiment sys tibble tidyr tidyselect txdbmaker tximport UCSC.utils utf8 vctrs withr XML xml2 XVector yaml

tximeta: transcript quantification import with automatic metadata

Rendered fromtximeta.Rmdusingknitr::rmarkdown

Last update: 2026-06-13
Started: 2018-07-12

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
Import transcript quantification with metadata	tximeta-package
Add CDS to rowRanges of a transcript-level SummarizedExperiment	addCDS
Add exons to rowRanges of a transcript-level SummarizedExperiment	addExons
Add IDs to rowRanges of a SummarizedExperiment	addIds
Get or set the directory of the BiocFileCache used by tximeta	getTximetaBFC setTximetaBFC
Import quantification across mixed reference transcripts	importData
Inspect digest matches from 'importData()' imported data	inspectDigests
Make and load linked transcriptomes (linked GTF and FASTA)	linkedTxome loadLinkedTxome makeLinkedTxome
Make linked transcript data (linked GRanges)	linkedTxpData makeLinkedTxpData
Make a DGEList from tximeta output	makeDGEList
Retrieve the cDNA transcript sequence for a SummarizedExperiment	retrieveCDNA
Retrieve the TxDb or EnsDb associated with a SummarizedExperiment	retrieveDb
Split SummarizedExperiment by gene categories	splitSE
Summarize estimated quantitites to gene-level	summarizeToGene,SummarizedExperiment-method
Import transcript quantification with metadata	tximeta
Update transcript metadatda for 'importData()' imported data	updateMetadata