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

Bioinformatics

Volumn 29, Issue 22, 2013, Pages 2943-2945

  Katayama, Shintaro ^a   Töhönen, Virpi ^a   Linnarsson, Sten ^a   Kere, Juha ^a  

^a KAROLINSKA INSTITUTE   (Sweden)

Author keywords

[No Author keywords available]

Indexed keywords

ARTICLE; GENE EXPRESSION PROFILING; HUMAN; METHODOLOGY; SEQUENCE ANALYSIS; SINGLE CELL ANALYSIS; STATISTICAL ANALYSIS; PROCEDURES;

DATA INTERPRETATION, STATISTICAL; GENE EXPRESSION PROFILING; HUMANS; SEQUENCE ANALYSIS, RNA; SINGLE-CELL ANALYSIS;

EID: 84890060756     PISSN: 13674803     EISSN: 14602059     Source Type: Journal    
DOI: 10.1093/bioinformatics/btt511     Document Type: Article

References (15)

1. Anders, S. and Huber, W. (2010) Differential expression analysis for sequence count data. Genome Biol., 11, R106.
2. Bullard, J.H. et al. (2010) Evaluation of statistical methods for normalization and differential expression in mRNA-Seq experiments. BMC Bioinformatics, 11, 94.
3. Chubb, J.R. et al. (2006) Transcriptional pulsing of a developmental gene. Curr. Biol., 16, 1018-1025.
4. Dobson, A.T. et al. (2004) The unique transcriptome through day 3 of human preimplantation development. Hum. Mol. Genet., 13, 1461-1470.
5. Hashimshony, T. et al. (2012) CEL-Seq: single-cell RNA-seq by multiplexed linear amplification. Cell Rep., 2, 666-673.
6. Islam, S. et al. (2011) Characterization of the single-cell transcriptional landscape by highly multiplex RNA-seq. Genome Res., 21, 1160-1167.
7. Islam, S. et al. (2012) Highly multiplexed and strand-specific single-cell RNA 50 end sequencing. Nat. Protoc., 7, 813-828.
8. Kivioja, T. et al. (2012) Counting absolute numbers of molecules using unique molecular identifiers. Nat. Methods, 9, 72-74.
9. Li, J. et al. (2011) Normalization, testing, and false discovery rate estimation for RNA-sequencing data. Biostatistics, 13, 523-538.
10. Li, J. and Tibshirani, R. (2011) Finding consistent patterns: a nonparametric approach for identifying differential expression in RNA-Seq data. Stat. Methods Med. Res. [Epub ahead of print, November 28, 2011].
11. Lovén, J. et al. (2012) Revisiting global gene expression analysis. Cell, 151, 476-482.
12. Raj, A. et al. (2006) Stochastic mRNA synthesis in mammalian cells. PLoS Biol., 4, e309.
13. Ramskö ld, D. et al. (2012) Full-length mRNA-Seq from single-cell levels of RNA and individual circulating tumor cells. Nat. Biotechnol., 30, 777-782.
14. Robinson, M.D. and Oshlack, A. (2010) A scaling normalization method for differential expression analysis of RNA-seq data. Genome Biol., 11, R25.
15. Tang, F. et al. (2011) Development and applications of single-cell transcriptome analysis. Nat. Methods, 8, S6-S11.