scPipe is a pipeline tool to preprocess single-cell RNA-seq data. The scPipe package has methods for barcode demultiplexing, read alignment, UMI-aware gene-level quantification, and quality control. It can use the following data from CEL-seq, MARS-seq, Drop-seq, Chromium 10x, and SMART-seq protocols.
Gene expression; RNA-seq; Sequencing
Tian L, Su S, Dong X, Amann-Zalcenstein D, Biben C, Seidi A, Hilton DJ, Naik SH, Ritchie ME "scPipe: A flexible R/Bioconductor preprocessing pipeline for single-cell RNA-sequencing data." PLoS Comput Biol. 2018 Aug 10;14(8):e1006361. eCollection 2018 Aug. https://doi.org/10.1371/journal.pcbi.1006361
PMID: 30096152
PMCID: PMC6105007
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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