ScPipe: A flexible R/Bioconductor preprocessing pipeline for single-cell RNA-sequencing data.

ABSTRACT: 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 t

SUBMITTER: Tian L 

PROVIDER: S-EPMC6105007 | biostudies-literature | 2018 Aug

REPOSITORIES: biostudies-literature