Welcome to the new bioconductor.org!

tximeta

Transcript Quantification Import with Automatic Metadata


Bioconductor version: Release (3.18)

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")):

Installation

To install this package, start R (version "4.3") 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.

Documentation

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

browseVignettes("tximeta")
Transcript quantification import with automatic metadata HTML R Script
Reference Manual PDF
NEWS Text

Details

biocViews Annotation, DataImport, FunctionalGenomics, GeneExpression, GenomeAnnotation, ImmunoOncology, Preprocessing, RNASeq, ReportWriting, ReproducibleResearch, SingleCell, Software, Transcription, Transcriptomics
Version 1.20.3
In Bioconductor since BioC 3.8 (R-3.5) (5.5 years)
License GPL-2
Depends
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
Enhances
Depends On Me rnaseqGene
Imports Me IsoformSwitchAnalyzeR
Suggests Me DESeq2, fishpond, fluentGenomics
Links To Me
Build Report Build Report

Package Archives

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

Source Package tximeta_1.20.3.tar.gz
Windows Binary tximeta_1.20.3.zip
macOS Binary (x86_64) tximeta_1.20.3.tgz
macOS Binary (arm64) tximeta_1.20.3.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/
Package Downloads Report Download Stats
Old Source Packages for BioC 3.18 Source Archive