tximport

This is the released version of tximport; for the devel version, see tximport.

All versions

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, 3.7, 3.6, 3.5, 3.4, 3.3

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

Bioconductor version: Release (3.23)

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")):

Michael Love, Charlotte Soneson, Mark Robinson. tximport: Import and summarize transcript-level estimates for transcript- and gene-level analysis. doi:10.18129/B9.bioc.tximport, R package version 1.40.0, https://bioconductor.org/packages/tximport.

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("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

Need some help? Ask on the Bioconductor Support site!

Details

biocViews	DataImport, GeneExpression, ImmunoOncology, Preprocessing, RNASeq, Software, Transcription, Transcriptomics
Version	1.40.0
In Bioconductor since	BioC 3.3 (R-3.3) (10.5 years)
License	LGPL (>=2)
Depends
Imports	utils, stats, methods
System Requirements
URL	https://github.com/thelovelab/tximport

Suggests	knitr, rmarkdown, testthat, tximportData, TxDb.Hsapiens.UCSC.hg19.knownGene, readr (>= 0.2.2), arrow, limma, edgeR (>= 4.9.2), DESeq2 (>= 1.11.6), rhdf5, jsonlite, matrixStats, Matrix, eds
Linking To
Enhances
Depends On Me
Imports Me	alevinQC, BgeeCall, CleanUpRNAseq, cpam, DifferentialRegulation, EventPointer, ExpHunterSuite, EZbakR, IsoformSwitchAnalyzeR, singleCellTK, TDbasedUFE, tximeta
Suggests Me	BANDITS, DESeq2, variancePartition
Links To Me
Build Report	Build Report, r-universe

Package Archives

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

Source Package	tximport_1.40.0.tar.gz
Windows Binary (x86_64)	tximport_1.40.0.zip
macOS Binary (big-sur-x86_64)	tximport_1.40.0.tgz
macOS Binary (sonoma-arm64)	tximport_1.40.0.tgz
Source Repository	git clone https://git.bioconductor.org/packages/tximport
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/tximport
Package Short Url	https://bioconductor.org/packages/tximport/
Package Downloads Report	Download Stats