scran is an R tool for single-cell RNA-seq data experiments. The scran algorithm has functions for low-level analyses of single-cell RNA-seq data, including normalization, the designation of the cell-cycle phase, and the determination of notably variable and significantly correlated gene expressions. Requires: SingleCellExperiment tool.
Cell biology; RNA-Seq
Lun AT, McCarthy DJ, Marioni JC "A step-by-step workflow for low-level analysis of single-cell RNA-seq data with Bioconductor." F1000Res. 2016 Aug 31;5:2122. 2016. https://doi.org/10.12688/f1000research.9501.2
PMID: 27909575
PMCID: PMC5112579
Huber W, Carey VJ, Gentleman R, Anders S, Carlson M, Carvalho BS, Bravo HC, Davis S, Gatto L, Girke T, Gottardo R, Hahne F, Hansen KD, Irizarry RA, Lawrence M, Love MI, MacDonald J1, Obenchain V, Oleś AK, Pagès H, Reyes A, Shannon P, Smyth GK, Tenenbaum D, Waldron L, Morgan M "Orchestrating high-throughput genomic analysis with Bioconductor." Nat Methods. 2015 Feb;12(2):115-21. https://doi.org/10.1038/nmeth.3252
PMID: 25633503
PMCID: PMC4509590
Gentleman RC, Carey VJ, Bates DM, Bolstad B, Dettling M, Dudoit S, Ellis B, Gautier L, Ge Y, Gentry J, Hornik K, Hothorn T, Huber W, Iacus S, Irizarry R, Leisch F, Li C, Maechler M, Rossini AJ, Sawitzki G, Smith C, Smyth G, Tierney L, Yang JY, Zhang J. "Bioconductor: open software development for computational biology and bioinformatics." Genome Biol. 2004;5(10):R80. Epub 2004 Sep 15. https://doi.org/10.1186/gb-2004-5-10-r80
PMID: 15461798
PMCID: PMC545600
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