tximport

DOI: 10.18129/B9.bioc.tximport    

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

Bioconductor version: Release (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")

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 1.12.3
In Bioconductor since BioC 3.3 (R-3.3) (3.5 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
SystemRequirements
Enhances
URL https://github.com/mikelove/tximport
Depends On Me
Imports Me alevinQC, BgeeCall, IsoformSwitchAnalyzeR, 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_1.12.3.tar.gz
Windows Binary tximport_1.12.3.zip (32- & 64-bit)
Mac OS X 10.11 (El Capitan) tximport_1.12.3.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
Old Source Packages for BioC 3.9 Source Archive

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