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

rna-seqRecent 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

  • Katayama S, Töhönen V, Linnarsson S, Kere J. (2013) SAMstrt: Statistical test for differential expression in single-cell transcriptome with spike-in normalization. Bioinformatics [Epub ahead of print]. [article]