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This is the development version of tximeta; for the stable release version, see tximeta.

Transcript Quantification Import with Automatic Metadata

Bioconductor version: Development (3.19)

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")):


To install this package, start R (version "4.4") and enter:

if (!require("BiocManager", quietly = TRUE))

# The following initializes usage of Bioc devel


For older versions of R, please refer to the appropriate Bioconductor release.


To view documentation for the version of this package installed in your system, start R and enter:

Transcript quantification import with automatic metadata HTML R Script
Reference Manual PDF


biocViews Annotation, DataImport, FunctionalGenomics, GeneExpression, GenomeAnnotation, ImmunoOncology, Preprocessing, RNASeq, ReportWriting, ReproducibleResearch, SingleCell, Software, Transcription, Transcriptomics
Version 1.21.4
In Bioconductor since BioC 3.8 (R-3.5) (5.5 years)
License GPL-2
Imports SummarizedExperiment, tximport, jsonlite, S4Vectors, IRanges, GenomicRanges, AnnotationDbi, GenomicFeatures, ensembldb, BiocFileCache, AnnotationHub, Biostrings, tibble, GenomeInfoDb, tools, utils, methods, Matrix
System Requirements
URL https://github.com/thelovelab/tximeta
See More
Suggests knitr, rmarkdown, testthat, tximportData, org.Dm.eg.db, DESeq2, fishpond, edgeR, limma, devtools
Linking To
Depends On Me rnaseqGene
Imports Me IsoformSwitchAnalyzeR
Suggests Me DESeq2, fishpond, fluentGenomics
Links To Me
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Package Archives

Follow Installation instructions to use this package in your R session.

Source Package tximeta_1.21.4.tar.gz
Windows Binary tximeta_1.21.4.zip
macOS Binary (x86_64) tximeta_1.21.4.tgz
macOS Binary (arm64) tximeta_1.21.4.tgz
Source Repository git clone https://git.bioconductor.org/packages/tximeta
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/tximeta
Bioc Package Browser https://code.bioconductor.org/browse/tximeta/
Package Short Url https://bioconductor.org/packages/tximeta/
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