SAMstrt
Computational Tool
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General Information
DescriptionStatistical test for differential expression in single-cell transcriptome with spike-in normalization
Homepagehttps://github.com/shka/R-SAMstrt
Publications
SAMstrt: statistical test for differential expression in single-cell transcriptome with spike-in normalization
Shintaro Katayama; Virpi Töhönen; Sten Linnarsson; Juha Kere
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.
DOI: https://doi.org/10.1093/bioinformatics/btt511
Metrics:
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