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tximport

Import and summarize transcript-level estimates for transcript- and gene-level analysis


Bioconductor version: Release (3.18)

Imports transcript-level abundance, estimated counts and transcript lengths, and summarizes into matrices for use with downstream gene-level analysis packages. Average transcript length, weighted by sample-specific transcript abundance estimates, is provided as a matrix which can be used as an offset for different expression of gene-level counts.

Author: Michael Love [cre,aut], Charlotte Soneson [aut], Mark Robinson [aut], Rob Patro [ctb], Andrew Parker Morgan [ctb], Ryan C. Thompson [ctb], Matt Shirley [ctb], Avi Srivastava [ctb]

Maintainer: Michael Love <michaelisaiahlove at gmail.com>

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

Installation

To install this package, start R (version "4.3") and enter:


if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

BiocManager::install("tximport")

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("tximport")
Importing transcript abundance datasets with tximport HTML R Script
Reference Manual PDF
NEWS Text

Details

biocViews DataImport, GeneExpression, ImmunoOncology, Preprocessing, RNASeq, Software, Transcription, Transcriptomics
Version 1.30.0
In Bioconductor since BioC 3.3 (R-3.3) (8 years)
License LGPL (>=2)
Depends
Imports utils, stats, methods
System Requirements
URL https://github.com/thelovelab/tximport
See More
Suggests knitr, rmarkdown, testthat, tximportData, TxDb.Hsapiens.UCSC.hg19.knownGene, readr (>= 0.2.2), arrow, limma, edgeR, DESeq2(>= 1.11.6), rhdf5, jsonlite, matrixStats, Matrix, eds
Linking To
Enhances
Depends On Me
Imports Me alevinQC, BgeeCall, DifferentialRegulation, EventPointer, ExpHunterSuite, IsoformSwitchAnalyzeR, singleCellTK, TDbasedUFE, tximeta
Suggests Me BANDITS, DESeq2, HumanTranscriptomeCompendium, SummarizedBenchmark, variancePartition
Links To Me
Build Report Build Report

Package Archives

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

Source Package tximport_1.30.0.tar.gz
Windows Binary tximport_1.30.0.zip
macOS Binary (x86_64) tximport_1.30.0.tgz
macOS Binary (arm64) tximport_1.30.0.tgz
Source Repository git clone https://git.bioconductor.org/packages/tximport
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/tximport
Bioc Package Browser https://code.bioconductor.org/browse/tximport/
Package Short Url https://bioconductor.org/packages/tximport/
Package Downloads Report Download Stats