SAMstrt: statistical test for differential expression in single-cell transcriptome with spike-in normalization.
basic_science · Level V
Where this comes from
- Record sourced from PubMed, PMID 23995393.
- Also identified by DOI 10.1093/bioinformatics/btt511 and PMC identifier 3810855.
- Licence recorded as CC BY.
- The licence permits redistribution, so the abstract is shown in full and the full text is available from the publisher.
Abstract
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
Medical subject headings
- Gene Expression Profiling
- Sequence Analysis, RNA