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Count-based differential expression analysis of RNA sequencing data using R and Bioconductor.
Anders S, McCarthy DJ, Chen Y, Okoniewski M, Smyth GK, Huber W, Robinson MD. Anders S, et al. Nat Protoc. 2013 Sep;8(9):1765-86. doi: 10.1038/nprot.2013.099. Epub 2013 Aug 22. Nat Protoc. 2013. PMID: 23975260
Testing significance relative to a fold-change threshold is a TREAT.
McCarthy DJ, Smyth GK. McCarthy DJ, et al. Bioinformatics. 2009 Mar 15;25(6):765-71. doi: 10.1093/bioinformatics/btp053. Epub 2009 Jan 28. Bioinformatics. 2009. PMID: 19176553 Free PMC article.
Detecting differential expression in RNA-sequence data using quasi-likelihood with shrunken dispersion estimates.
Lund SP, Nettleton D, McCarthy DJ, Smyth GK. Lund SP, et al. Stat Appl Genet Mol Biol. 2012 Oct 22;11(5):/j/sagmb.2012.11.issue-5/1544-6115.1826/1544-6115.1826.xml. doi: 10.1515/1544-6115.1826. Stat Appl Genet Mol Biol. 2012. PMID: 23104842
Classification of low quality cells from single-cell RNA-seq data.
Ilicic T, Kim JK, Kolodziejczyk AA, Bagger FO, McCarthy DJ, Marioni JC, Teichmann SA. Ilicic T, et al. Genome Biol. 2016 Feb 17;17:29. doi: 10.1186/s13059-016-0888-1. Genome Biol. 2016. PMID: 26887813 Free PMC article.
f-scLVM: scalable and versatile factor analysis for single-cell RNA-seq.
Buettner F, Pratanwanich N, McCarthy DJ, Marioni JC, Stegle O. Buettner F, et al. Genome Biol. 2017 Nov 7;18(1):212. doi: 10.1186/s13059-017-1334-8. Genome Biol. 2017. PMID: 29115968 Free PMC article.
[No authors listed] [No authors listed] PMID: 27917286
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