BASiCS (Bayesian Analysis of Single-Cell Sequencing), is a tool for the analysis of single-cell RNA-seq data. The BASiCS algorithm uses a Bayesian hierarchical approach in supervised experiments. It estimates cell-specific normalization parameters from the model. It can quantify technical variability using spiking genes included in a cell's lysate, and it reports the total variability as experimental and biological components. Requires: SingleCellExperiment.
Cell biology; Gene expression; RNA-seq; Sequencing; Transcriptomics
Vallejos CA, Marioni JC, Richardson S "BASiCS: Bayesian Analysis of Single-Cell Sequencing Data." PLoS Comput Biol. 2015 Jun 24;11(6):e1004333. eCollection 2015 Jun. https://doi.org/10.1371/journal.pcbi.1004333
PMID: 26107944
PMCID: PMC4480965
Eling N, Richard AC, Richardson S, Marioni JC, Vallejos CA "Correcting the Mean-Variance Dependency for Differential Variability Testing Using Single-Cell RNA Sequencing Data." Cell Syst. 2018 Sep 26;7(3):284-294.e12. https://doi.org/10.1016/j.cels.2018.06.011
PMID: 30172840
PMCID: PMC6167088
Vallejos CA, Richardson S, Marioni JC "Beyond comparisons of means: understanding changes in gene expression at the single-cell level." Genome Biol. 2016 Apr 15;17:70. https://doi.org/10.1186/s13059-016-0930-3
PMID: 27083558
PMCID: PMC4832562
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
If you find errors, please report here.
SECTIONS
TutorialsFind thousands of Bioinformatics and Life Science software tools and databases in the newly launched
Ads