RNA-Seq: SAMstrt: Statistical test for differential expression in single-cell transcr
 

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

Bioinformatics. 2013 Aug 31;

Authors: Katayama S, Töhönen V, Linnarsson S, Kere J

Abstract
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 file contain the SAMstrt code, several sample codes and input data for the figures.


PMID: 23995393 [PubMed - as supplied by publisher]



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