I’m currently developing a single-cell RNA Sequencing pipeline for NetworkAnalyst; an open source, web-based platform for comprehensive gene expression profiling & meta-analysis. The website uses mostly R code (via {RServe}📦 ), Java for the heavy-lifting and Javascript for data visualization. Developing this pipeline I’ve been applying various profiling and timing tools to optimize R code and would like to share my experiences.

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We decided to use the {Seurat} 📦 from the Satija Lab because it is one of the most comprehensive packages for end-to-end scRNA-Seq analysis (it includes tools for QC, analysis, visualization, clustering, DE analysis, analysis of spatial data etc.). …

About

Matt.0

#Datascientist working on #Bioinformatics and #Epigenetics. Blogs about #rstats at https://www.r-bloggers.com

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