Single-Cell RNA-Seq: Analysis on the Palantir Platform (Jan. 29th, Frederick)

About this Class

Single-cell RNA sequencing (scRNA-Seq) is a rapidly evolving method in the field of single-cell genomics which has enhanced our ability to study biological processes at the cellular level. The CCR Collaborative Bioinformatics Resource (CCBR) has implemented a Seurat-based Single-cell RNA-seq workflow on the Palantir collaboration platform, which is available and free to use for all NCI researchers. The platform allows users to explore and build their analyses in a graphical environment. For researchers who are conversant in code, or who are interested in learning, all of the workflow code is easily viewable and modifiable, as well. This training session will include a brief lecture on the history and theory behind Single-cell RNA-seq.  Most of the class time will be devoted to a workshop in which trainees will be guided through a basic analysis of a real single-cell dataset.  Topics you will learn about include filtering and QC, PCA and merging of Seurat objects, clustering, cell annotation, coloring of UMAP and TSNE plots by various metadata, and differential expression.  After training, trainees will be ready to upload their own data to the platform and begin their own analyses. Trainees will need an NIH laptop capable of connecting to the secure NIH wireless network, as well as their own NIH credentials.