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To install this package, start R and enter:
## try http:// if https:// URLs are not supported
source("https://bioconductor.org/biocLite.R")
biocLite("tximport")
In most cases, you don't need to download the package archive at all.
tximport
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Import and summarize transcript-level estimates for transcript- and gene-level analysis
Bioconductor version: Release (3.5)
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:
## try http:// if https:// URLs are not supported
source("https://bioconductor.org/biocLite.R")
biocLite("tximport")
Documentation
| HTML | R Script | Importing transcript abundance datasets with tximport |
| Reference Manual | ||
| Text | NEWS |
Details
| biocViews | DataImport, GeneExpression, RNASeq, Software, Transcription |
| Version | 1.4.0 |
| In Bioconductor since | BioC 3.3 (R-3.3) (1.5 years) |
| License | GPL (>=2) |
| Depends | |
| Imports | utils |
| LinkingTo | |
| Suggests | knitr, rmarkdown, testthat, tximportData, TxDb.Hsapiens.UCSC.hg19.knownGene, readr (>= 0.2.2), limma, edgeR, DESeq2(>= 1.11.6), rhdf5, rjson |
| SystemRequirements | |
| Enhances | |
| URL | |
| Depends On Me | |
| Imports Me | scater |
| Suggests Me | DESeq2, variancePartition |
| Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | tximport_1.4.0.tar.gz |
| Windows Binary | tximport_1.4.0.zip |
| Mac OS X 10.11 (El Capitan) | tximport_1.4.0.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/tximport |
| Package Short Url | http://bioconductor.org/packages/tximport/ |
| Package Downloads Report | Download Stats |
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