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

Package: tximport 1.41.0

Michael Love

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

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.

Authors: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]

tximport_1.41.0.tar.gz
tximport_1.41.0.zip(r-4.7)tximport_1.41.0.zip(r-4.6)tximport_1.41.0.zip(r-4.5)
tximport_1.41.0.tgz(r-4.6-any)tximport_1.41.0.tgz(r-4.5-any)
tximport_1.41.0.tar.gz(r-4.7-any)tximport_1.41.0.tar.gz(r-4.6-any)
tximport_1.41.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
tximport/json (API)

# Install 'tximport' in R:

install.packages('tximport', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/thelovelab/tximport/issues

On BioConductor:tximport-1.41.0(bioc 3.24)tximport-1.40.0(bioc 3.23)

dataimport preprocessing rnaseq transcriptomics transcription geneexpression immunooncology bioconductor deseq2

12.94 score 145 stars 12 packages 5.6k scripts 367 mentions 3 exports 0 dependencies

Last updated from:5feefe5f26. Checks:1 ERROR, 9 OK. Indexed: yes.

Target	Result	Time
bioc-checks	ERROR	224
linux-devel-x86_64	OK	332
source / vignettes	OK	331
linux-release-x86_64	OK	310
macos-release-arm64	OK	154
macos-oldrel-arm64	OK	137
windows-devel	OK	605
windows-release	OK	578
windows-oldrel	OK	586
wasm-release	OK	222

Exports:makeCountsFromAbundance summarizeToGene tximport

Dependencies:

Importing transcript abundance with tximport

Rendered fromtximport.Rmdusingknitr::rmarkdown

Help page	Topics
Tximport package: import transcript-level quantification data	tximport-package
Low-level function to make counts from abundance using matrices	makeCountsFromAbundance
Summarize estimated quantitites to gene-level	summarizeToGene summarizeToGene,list-method
Import transcript-level abundances and counts for transcript- and gene-level analysis packages	tximport

Help page

Topics

Tximport package: import transcript-level quantification data

tximport-package

Low-level function to make counts from abundance using matrices

makeCountsFromAbundance

Summarize estimated quantitites to gene-level

summarizeToGene summarizeToGene,list-method

Import transcript-level abundances and counts for transcript- and gene-level analysis packages

tximport