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Bioconductor - tximport (development version)

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 (3.22)

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 "4.5") and enter:


if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

# The following initializes usage of Bioc devel
BiocManager::install(version='devel')

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

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

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