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Love, Mark D. Robinson.\n[Differential analyses for RNA-seq: transcript-level estimates improve gene-level inferences](http://f1000research.com/articles/4-1521),\n*F1000Research*, 4:1521, December 2015. doi: 10.12688/f1000research.7563.1\n\n---\n\nImports transcript-level abundance, estimated counts and \ntranscript lengths, and summarizes into matrices for use with downstream\nstatistical analysis packages such as edgeR, DESeq2, limma-voom. \nAverage transcript length, weighted by \nsample-specific transcript abundance estimates, is provided as a matrix\nwhich can be used as an offset for different expression of \ngene-level counts.\n\nSee examples in the [vignette](http://bioconductor.org/packages/release/bioc/vignettes/tximport/inst/doc/tximport.html).\n\nNotes:\n\n* tximport as of version 1.3.9 will import inferential replicates\n  (Gibbs samples or bootstrap samples) from Salmon, Sailfish or kallisto.\n* Though we provide here functionality for performing gene-level\n  differential expression using summarized transcript-level estimates,\n  this is does not mean we suggest that users *only* perform gene-level\n  analysis. Gene-level differential expression can be complemented\n  with transcript- or exon-level analysis. The argument `txOut=TRUE`\n  can be used to generate transcript-level matrices.\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fthelovelab%2Ftximport","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fthelovelab%2Ftximport","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fthelovelab%2Ftximport/lists"}