tximeta
This is the released version of tximeta; for the devel version, see tximeta.
All Bioconductor versions of tximeta
3.24 (devel), 3.23 (release), 3.22, 3.21, 3.20, 3.19, 3.18, 3.17, 3.16, 3.15, 3.14, 3.13, 3.12, 3.11, 3.10, 3.9, 3.8
Transcript Quantification Import with Automatic Metadata
Bioconductor version: 3.23 · Package version: 1.30.0
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.
Author: Michael Love [aut, cre], Charlotte Soneson [aut, ctb], Peter Hickey [aut, ctb], Rob Patro [aut, ctb], NIH NHGRI [fnd], CZI [fnd]
Maintainer: Michael Love <michaelisaiahlove at gmail.com>
Citation
From within R, enter citation("tximeta"):
Michael Love, Charlotte Soneson, Peter Hickey, Rob Patro. tximeta: Transcript Quantification Import with Automatic Metadata. doi:10.18129/B9.bioc.tximeta, R package version 1.30.0, https://bioconductor.org/packages/tximeta.
Generated from the package metadata; it may differ from the package's own citation.
Installation
To install this package, start R (version "4.6") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("tximeta")For older versions of R, please refer to the appropriate Bioconductor release.
Details
| Version | 1.30.0 |
| License | GPL-2 |
| URL | https://github.com/thelovelab/tximeta |
| Last updated | 2026-04-28 |
| In Bioconductor since | BioC 3.8 (R-3.5) (7 years) |
| Downloads rank | 200 of 2,418 |
| Source branch | RELEASE_3_23 |
| Build report | Bioconductor build system, r-universe |
| biocViews | Annotation, DataImport, FunctionalGenomics, GeneExpression, GenomeAnnotation, ImmunoOncology, LongRead, Preprocessing, RNASeq, ReportWriting, ReproducibleResearch, SingleCell, Software, Transcription, Transcriptomics |
| Package Short Url | https://bioconductor.org/packages/tximeta/ |
Documentation
To view documentation for the version of this package installed in your system, start R and enter:
browseVignettes("tximeta")| tximeta: transcript quantification import with automatic metadata | HTML | R Script |
| Reference Manual | ||
| NEWS | Text |
Download
Follow the installation instructions to use this package in your R session.
| Source package | tximeta_1.30.0.tar.gz |
| Windows binary (x86_64) | tximeta_1.30.0.zip |
| macOS binary (arm64) | tximeta_1.30.0.tgz |
| macOS binary (x86_64) | tximeta_1.30.0.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/tximeta |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/tximeta |
| Package Downloads Report | Download Stats |
Dependencies
Depends: R (>= 4.1.0)
Imports: SummarizedExperiment (>= 1.39.1), tximport, jsonlite, S4Vectors, IRanges, GenomicRanges (>= 1.61.1), AnnotationDbi, DBI, GenomicFeatures, txdbmaker, ensembldb, BiocFileCache, AnnotationHub, Biostrings, tibble, Seqinfo, tools, utils, methods, Matrix
Suggests: knitr, rmarkdown, testthat, tximportData (>= 1.37.5), org.Dm.eg.db, DESeq2, edgeR (>= 4.9.2), limma, devtools, macrophage
Reverse dependencies
Depends On Me (1): rnaseqGene
Imports Me (1): IsoformSwitchAnalyzeR
Suggests Me (3): DESeq2, fishpond, fluentGenomics