BTEP Getting Started with scRNA-Seq Seminar Series

This talk will cover a scRNA-seq workflow available to NCI researchers on NIDAP. NIDAP, the NIH Integrated Data Analysis Platform, is a cloud-based and collaborative data aggregation and analysis platform that hosts user-friendly bioinformatics workflows. This platform allows researchers to use many of the open-source tools discussed in this seminar series without necessitating coding experience. This seminar will focus on the capabilities of this workflow for QC, annotation, and visualization of single-cell RNA-seq data.

This seminar provides an overview of differential expression testing with Seurat. Topics to be covered include preparing data for differential gene expression, differential gene analysis between specific groups, differential gene analysis for cluster classification, SingleR for cell type annotation, and visualizing genes of interest.  

This lesson reviews many of the standard steps in a scRNA-Seq workflow: QC filtering, normalization, scaling, and clustering. 

This seminar provides an introduction to R in the context of single cell RNA-Seq analysis with Seurat.  In this seminar, attendees will learn about options for analyzing scRNA-Seq data, resources for learning R, how to import scRNA-Seq data, and how to create, examine, and access data stored in a Seurat object.  

Kimia Dadkhah, bioinformatics analyst (SCAF), will talk about Cell Ranger output and essential quality control metrics in single cell data analysis, how to interpret these and make informed decisions, and other considerations to keep in mind when assessing the quality of returned data from SCAF.  

Single cell RNA sequencing (scRNA-Seq) is becoming increasingly more common in biomedical research, but what is scRNA-Seq? How does it differ from other transcriptomic approaches (e.g., bulk RNA-Seq), and what are the potential applications, technologies, and workflows? This presentation will introduce learners to scRNA-Seq, answering the above and touching on additional topics such as methodological challenges, concerns, and best practices.  

The Single Cell Analysis Facility (SCAF) is a CCR facility dedicated to the application of single-cell technologies in cancer research. Based on the NIH Bethesda main campus, SCAF aims to provide the broadest range of project support from consultation on experimental design, sequencing, and data analysis. Learn more about SCAF and the single-cell genomics technologies available to CCR investigators in this overview presentation.