tximport: Import and summarize transcript-level estimates for transcript- and gene-level analysis
Version 1.4.0

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.

AuthorMichael Love [cre,aut], Charlotte Soneson [aut], Mark Robinson [aut], Rob Patro [ctb], Andrew Parker Morgan [ctb], Ryan C. Thompson [ctb], Matt Shirley [ctb]
Bioconductor views DataImport GeneExpression RNASeq Transcription
Date of publicationNone
MaintainerMichael Love <michaelisaiahlove@gmail.com>
LicenseGPL (>=2)
Version1.4.0
Package repositoryView on Bioconductor
InstallationInstall the latest version of this package by entering the following in R:
source("https://bioconductor.org/biocLite.R")
biocLite("tximport")

Getting started

README.md
Importing transcript abundance datasets with tximport

Popular man pages

tximport: Import transcript-level abundances and counts for transcript-...
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All man pages Function index File listing

Man pages

tximport: Import transcript-level abundances and counts for transcript-...

Functions

RowVar Source code
makeCountsFromAbundance Source code
readInfRepFish Source code
readInfRepKallisto Source code
read_kallisto_h5 Source code
replaceMissingLength Source code
summarizeFail Source code
summarizeToGene Man page Source code
tximport Man page Source code

Files

DESCRIPTION
NAMESPACE
NEWS
R
R/helper.R
R/infReps.R
R/summarizeToGene.R
R/tximport.R
README.md
build
build/vignette.rds
inst
inst/CITATION
inst/doc
inst/doc/tximport.R
inst/doc/tximport.Rmd
inst/doc/tximport.html
man
man/tximport.Rd
tests
tests/testthat
tests/testthat.R
tests/testthat/test_counts_from_abundance.R
tests/testthat/test_h5.R
tests/testthat/test_kallisto.R
tests/testthat/test_no_tx2gene.R
tests/testthat/test_one_sample.R
tests/testthat/test_rsem.R
tests/testthat/test_salmon.R
vignettes
vignettes/library.bib
vignettes/tximport.Rmd
tximport documentation built on May 20, 2017, 10:25 p.m.

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