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Single-cell RNA sequencing has led to unprecedented levels of data complexity. Although several computational platforms are available, performing data analyses for multiple datasets remains a significant challenge. Here, we provide a comprehensive analytical protocol to interrogate multiple datasets on SingCellaR, an analysis package in R. This tool can be applied to general single-cell transcriptome analyses. We demonstrate steps for data analyses and visualization using bespoke pipelines, in conjunction with existing analysis tools to study human hematopoietic stem and progenitor cells. For complete details on the use and execution of this protocol, please refer to Roy et al. (2021).

Original publication




Journal article


STAR Protoc

Publication Date





Bioinformatics, RNAseq, Single Cell, Stem Cells, Systems biology, Data Analysis, Humans, RNA-Seq, Single-Cell Analysis, Transcriptome, Whole Exome Sequencing