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

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Katayama S, Töhönen V, Linnarsson S, Kere J

Bioinformatics 29 (22) 2943-2945 [2013-11-15; online 2013-08-31]

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. SAMstrt is implemented on R and available in github (https://github.com/shka/R-SAMstrt). shintaro.katayama@ki.se

Affiliated researcher

PubMed 23995393

DOI 10.1093/bioinformatics/btt511

Crossref 10.1093/bioinformatics/btt511

pii: btt511
pmc: PMC3810855