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Transcript Quantification Import with Automatic Metadata

Bioconductor version: Release (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>

Citation (from within R, enter citation("tximeta")):


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

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


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 1.22.1
In Bioconductor since BioC 3.8 (R-3.5) (5.5 years)
License GPL-2
Imports SummarizedExperiment, tximport, jsonlite, S4Vectors, IRanges, GenomicRanges, AnnotationDbi, GenomicFeatures, txdbmaker, ensembldb, BiocFileCache, AnnotationHub, Biostrings, tibble, GenomeInfoDb, tools, utils, methods, Matrix
System Requirements
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Suggests knitr, rmarkdown, testthat, tximportData,, 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_1.22.1.tar.gz
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macOS Binary (x86_64) tximeta_1.22.1.tgz
macOS Binary (arm64) tximeta_1.22.1.tgz
Source Repository git clone
Source Repository (Developer Access) git clone
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Old Source Packages for BioC 3.19 Source Archive