sincell is an R tool for the assessment of cell-state hierarchies in single-cell RNA-seq (scRNA-seq) datasets. The package includes functions to compute cell-state hierarchies, statistics, accounts for random variations in the data, functional association tests, and graphics.
Transcriptomics; RNA-seq; RNA; Taxonomy
Juliá M, Telenti A, Rausell A "Sincell: an R/Bioconductor package for statistical assessment of cell-state hierarchies from single-cell RNA-seq." Bioinformatics 2015; 31(20):3380-2 https://doi.org/10.1093/bioinformatics/btv368
PMID: 26099264
PMCID: PMC4595899
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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