Oscope is a tool for the identification of oscillatory genes single-cell RNA-seq data. The package has functions for searching candidate oscillatory pairs, k-medoids clustering, and to recover the base cycle order for oscillatory groups.
Gene regulation; RNA-Seq; Gene expression
Leng N, Chu LF, Barry C, Li Y, Choi J, Li X, Jiang P, Stewart RM, Thomson JA, Kendziorski C "Oscope identifies oscillatory genes in unsynchronized single-cell RNA-seq experiments." Nat Methods. 2015 Oct;12(10):947-950. https://doi.org/10.1038/nmeth.3549
PMID: 26301841
PMCID: PMC4589503
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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