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

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

SUBMITTER: Katayama S 

PROVIDER: S-EPMC3810855 | biostudies-other | 2013 Nov

REPOSITORIES: biostudies-other

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

Katayama Shintaro S   Töhönen Virpi V   Linnarsson Sten S   Kere Juha J  

Bioinformatics (Oxford, England) 20130831 22

<h4>Motivation</h4>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.<h4>Availability and implem  ...[more]