Skip to content
Import and summarize transcript-level estimates for gene-level analysis
Branch: master
Clone or download
Latest commit d7082ef Dec 1, 2019
Type Name Latest commit message Commit time
Failed to load latest commit information.
R fix link Dec 2, 2019
inst Adding tximport Feb 10, 2016
man fix link Dec 2, 2019
tests new readEDS code updates to make Aug 7, 2019
vignettes fix vignette more Sep 26, 2019
.gitignore merge Dec 8, 2017 adding code of conduct Nov 15, 2019
DESCRIPTION fix link Dec 2, 2019
NAMESPACE adding fast alevin importer from fishpond Aug 6, 2019
NEWS update news Oct 18, 2019 correct links from README Mar 8, 2017


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

Description of methods and analysis described in:

Imports transcript-level abundance, estimated counts and transcript lengths, and summarizes into matrices for use with downstream statistical analysis packages such as edgeR, DESeq2, limma-voom. 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.

See examples in the vignette.


  • tximport as of version 1.3.9 will import inferential replicates (Gibbs samples or bootstrap samples) from Salmon, Sailfish or kallisto.
  • Though we provide here functionality for performing gene-level differential expression using summarized transcript-level estimates, this is does not mean we suggest that users only perform gene-level analysis. Gene-level differential expression can be complemented with transcript- or exon-level analysis. The argument txOut=TRUE can be used to generate transcript-level matrices.
You can’t perform that action at this time.