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 (3.9)

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 "3.6") and enter:

if (!requireNamespace("BiocManager", quietly = TRUE))
    install.packages("BiocManager")
BiocManager::install("tximport", version = "3.9")

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 1.11.7
In Bioconductor since BioC 3.3 (R-3.3) (3 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
SystemRequirements
Enhances
URL https://github.com/mikelove/tximport
Depends On Me
Imports Me alevinQC, IsoformSwitchAnalyzeR, tximeta
Suggests Me DESeq2, SummarizedBenchmark, variancePartition
Links To Me
Build Report  

Package Archives

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

Source Package tximport_1.11.7.tar.gz
Windows Binary tximport_1.11.7.zip (32- & 64-bit)
Mac OS X 10.11 (El Capitan) tximport_1.11.7.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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