# tximport Import and summarize transcript-level estimates for transcript- and 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](http://f1000research.com/articles/4-1521), *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 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](http://bioconductor.org/packages/release/bioc/vignettes/tximport/inst/doc/tximport.html). Notes: * 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.