SAMstrt: statistical test for differential expression in single-cell transcriptome with spike-in normalization

Motivation: Recent transcriptome studies have revealed that total transcript numbers vary by cell type and condition; therefore, the statistical assumptions for single-cell transcriptome studies must be revisited. SAMstrt is an extension code for SAMseq, which is a statistical method for differential expression, to enable spike-in normalization and statistical testing based on the estimated absolute number of transcripts per cell for single-cell RNA-seq methods. Availability and Implementation: SAMstrt is implemented on R and available in github (https://github.com/shka/R-SAMstrt). Contact: shintaro.katayama@ki.se Supplementary Information: Supplementary data are available at Bioinformatics online.