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  • 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. The scPipe R package is available for download from https://www.bioconductor.org/packages/scPipe. In the remainder of this article we provide an overview of the main features of our scPipe software and demonstrate its use on various in-house generated and publicly available scRNA-seq datasets. scPipe is an R [13] / Bioconductor [14] package that can handle data generated from all popular 3’ end scRNA-seq protocols and their variants, such as CEL-seq, MARS-seq, Chromium 10X and Drop-seq. The scPipe package is written in R and C++ and uses the Rcpp package [16, 17] to wrap the C++ code into R functions and the Rhtslib package [18] for BAM input/output. The scPipe package is available from https://www.bioconductor.org/packages/scPipe.
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