batchelor is an R tool for batch correction in single-cell RNA-seq data. The batchelor algorithm uses mutual nearest neighbors (MNNs) method in the high-dimensional expression space for the detection of batch effects. The algorithm does not depend on predefined population compositions. Requires: SingleCellExperiment.
RNA-seq; Transcriptomics
Haghverdi L, Lun ATL, Morgan MD, Marioni JC "Batch effects in single-cell RNA-sequencing data are corrected by matching mutual nearest neighbors." Nat Biotechnol. 2018 Jun;36(5):421-427. https://doi.org/10.1038/nbt.4091
PMID: 29608177
PMCID: PMC6152897
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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