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scPipe is an R package that allows barcode demultiplexing, transcript mapping and quality control of raw sequencing data generated by multiple 3 prime end sequencing protocols including CEL-seq, MARS-seq, Chromium 10x and Drop-seq. scPipe produces a count matrix that is essential for downstream analysis along with a user-friendly HTML report that summarises data quality. These results can be used as input for downstream analyses including normalization, visualization and statistical testing.

The package is under active development. Feel free to ask any questions or submit a pull request.


From Bioconductor

if (!requireNamespace("BiocManager", quietly=TRUE))

From GitHub (Developmental version)


Getting started

The general workflow of scPipe is illustrated in the following figure:

Data Preprocessing

For further examples see the vignette.


This package is inspired by the scater and scran packages. The idea to put cell barcode and UMI sequences into the BAM file is from Drop-seq tools. We thank Dr Aaron Lun for suggestions on package development.

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scPipe documentation built on Nov. 8, 2020, 8:28 p.m.