DropletUtils is a utility tool for the analysis of single-cell RNA-seq (scRNA-seq) data from droplet technologies. DropletUtils includes functions for loading, identification of empty droplets, removal of barcode-swapped pseudo-cells, and downsampling of the count matrix.
Gene expression; RNA-seq; Sequencing; Transcriptomics
Griffiths JA, Richard AC, Bach K, Lun ATL, Marioni JC "Detection and Removal of Barcode Swapping in Single-Cell RNA-seq Data " Nat Commun. 2018 Jul 10;9(1):2667. https://doi.org/10.1038/s41467-018-05083-x.
PMID: 29991676
PMCID: PMC6039488
Lun ATL, Riesenfeld S, Andrews T, Dao TP, Gomes T; participants in the 1st Human Cell Atlas Jamboree, Marioni JC "EmptyDrops: Distinguishing Cells From Empty Droplets in Droplet-Based Single-Cell RNA Sequencing Data " Genome Biol. 2019 Mar 22;20(1):63. https://doi.org/10.1186/s13059-019-1662-y
PMID: 30902100
PMCID: PMC6431044
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