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, 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.

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.