tximport

DOI: 10.18129/B9.bioc.tximport    

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

Bioconductor version: Release (3.13)

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>

Installation

To install this package, start R (version "4.1") and enter:

if (!requireNamespace("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")

 

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

Details

biocViews	DataImport, GeneExpression, ImmunoOncology, Preprocessing, RNASeq, Software, Transcription, Transcriptomics
Version	1.20.0
In Bioconductor since	BioC 3.3 (R-3.3) (5.5 years)
License	GPL (>=2)
Depends
Imports	utils, stats, methods
LinkingTo
Suggests	knitr, rmarkdown, testthat, tximportData, TxDb.Hsapiens.UCSC.hg19.knownGene, readr (>= 0.2.2), limma, edgeR, DESeq2(>= 1.11.6), rhdf5, jsonlite, matrixStats, Matrix, fishpond
SystemRequirements
Enhances
URL	https://github.com/mikelove/tximport
Depends On Me
Imports Me	alevinQC, BgeeCall, EventPointer, IsoformSwitchAnalyzeR, singleCellTK, tximeta
Suggests Me	BANDITS, DESeq2, HumanTranscriptomeCompendium, SummarizedBenchmark, variancePartition
Links To Me
Build Report

Package Archives

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

Source Package	tximport_1.20.0.tar.gz
Windows Binary	tximport_1.20.0.zip
macOS 10.13 (High Sierra)	tximport_1.20.0.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