Bioinformatics Training and Education Program

BTEP Getting Started with scRNA-Seq Seminar Series

2024 Seminar Series

This is a mini seminar series designed to help attendees learn more about single cell RNA-Seq, from applicable technologies to data analysis.

Event Documentation:

The CCBR Single-cell RNA-seq Workflow on NIDAP

  • When: May 29, 2024
  • Delivery: Online
  • Presented By: Joshua Meyer (CCBR)
  • 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.

Differential Expression Analysis with Seurat Archived

  • When: May 22, 2024
  • Delivery: Online
  • Presented By: Nathan Wong (CCBR)
  • 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.  



Getting Started with Seurat: QC to Clustering Archived

  • When: May 1, 2024
  • Delivery: Online
  • Presented By: Alex Emmons (BTEP)
  • This lesson reviews many of the standard steps in a scRNA-Seq workflow: QC filtering, normalization, scaling, and clustering. 

Introduction to scRNA-Seq with R (Seurat) Archived

  • When: April 24, 2024
  • Delivery: Online
  • Presented By: Alex Emmons (BTEP)
  • 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.  

SCAF: Overview of Cell Ranger output files and single cell data analysis quality control Archived

  • When: April 17, 2024
  • Delivery: Online
  • Presented By: Kimia Dadkhah (SCAF)
  • 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.  

Introduction to single cell RNA-Seq Archived

  • When: April 10, 2024
  • Delivery: Online
  • Presented By: Charlie Seibert, Saeed Yadranji Aghdam
  • 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 CCR Single Cell Analysis Facility (SCAF): An Overview Archived

  • When: April 3, 2024
  • Delivery: Online
  • Presented By: Mike Kelly (SCAF)
  • 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.