tximport is now hosted on Bioconductor. Be aware that this GitHub repo is therefore not up to date with the current version available here:

http://bioconductor.org/packages/tximport

tximport will become part of the Bioconductor release branch in April 2016. The latest version of tximport can be installed via:

source("http://bioconductor.org/biocLite.R")
biocLite("tximport")

Although, these installation steps will only be available for R-devel until April 2016, at which point, this will also work for the latest version of R.

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

Description of methods and analysis described in:

• Charlotte Soneson, Michael I. Love, Mark D. Robinson. Differential analyses for RNA-seq: transcript-level estimates improve gene-level inferences, F1000Research, 4:1521, December 2015. doi: 10.12688/f1000research.7563.1

Imports transcript-level abundance, estimated counts and transcript lengths, and summarizes into matrices for use with downstream gene-level 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 vignette

Notes:

• tximport does not import the bootstrap estimates from kallisto, Salmon, or Sailfish
• 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.