tximport

DOI: 10.18129/B9.bioc.tximport    

This is the development version of tximport; for the stable release version, see tximport.

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

Bioconductor version: Development (3.8)

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]

Maintainer: Michael Love <michaelisaiahlove at gmail.com>

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

Installation

To install this package, start R and enter:

if (!requireNamespace("BiocManager", quietly = TRUE))
    install.packages("BiocManager")
BiocManager::install("tximport", version = "devel")

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, RNASeq, Software, Transcription
Version 1.9.12
In Bioconductor since BioC 3.3 (R-3.3) (2.5 years)
License GPL (>=2)
Depends
Imports utils, stats
LinkingTo
Suggests knitr, rmarkdown, testthat, tximportData, TxDb.Hsapiens.UCSC.hg19.knownGene, readr (>= 0.2.2), limma, edgeR, DESeq2(>= 1.11.6), rhdf5, jsonlite, matrixStats
SystemRequirements
Enhances
URL
Depends On Me
Imports Me IsoformSwitchAnalyzeR, tximeta
Suggests Me DESeq2, scater, SummarizedBenchmark, variancePartition
Links To Me
Build Report  

Package Archives

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

Source Package tximport_1.9.12.tar.gz
Windows Binary tximport_1.9.12.zip
Mac OS X 10.11 (El Capitan) tximport_1.9.12.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 http://bioconductor.org/packages/tximport/
Package Downloads Report Download Stats

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