scPipe: A flexible R/Bioconductor preprocessing pipeline for single-cell RNA-sequencing data
Publication Year 2018-08-10, Volume 14, Issue #8, Page e1006361
Journal Title
PLoS Computational Biology
Publication Type
Journal Article
Single-cell RNA sequencing (scRNA-seq) technology allows researchers to profile the transcriptomes of thousands of cells simultaneously. Protocols that incorporate both designed and random barcodes have greatly increased the throughput of scRNA-seq, but give rise to a more complex data structure. There is a need for new tools that can handle the various barcoding strategies used by different protocols and exploit this information for quality assessment at the sample-level and provide effective visualization of these results in preparation for higher-level analyses. To this end, we developed scPipe, an R/Bioconductor package that integrates barcode demultiplexing, read alignment, UMI-aware gene-level quantification and quality control of raw sequencing data generated by multiple protocols that include CEL-seq, MARS-seq, Chromium 10X, Drop-seq and Smart-seq. scPipe produces a count matrix that is essential for downstream analysis along with an HTML report that summarises data quality. These results can be used as input for downstream analyses including normalization, visualization and statistical testing. scPipe performs this processing in a few simple R commands, promoting reproducible analysis of single-cell data that is compatible with the emerging suite of open-source scRNA-seq analysis tools available in R/Bioconductor and beyond. The scPipe R package is available for download from
WEHI Research Division(s)
Molecular Medicine
PubMed ID
Open Access at Publisher's Site
NHMRC Grants
NHMRC/1143163 NHMRC/1124812 NHMRC/1062820
Rights Notice
Refer to copyright notice on published article.

Creation Date: 2018-08-15 03:28:54
Last Modified: 2018-08-17 08:44:19
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