University of Southern California Single-Cell Omics Research and Education (USC-SCORE) is dedicated to driving excellence in the field of single-cell omics. We focus on applying and developing advanced methodologies to explore gene expression, epigenetics, proteomics, and spatial biology at the single-cell resolution. Our community is committed to training the next generation of scientists through workshops, seminars, and collaborative projects. We strive to uncover new insights into cellular diversity and its implications for personalized medicine and therapeutic innovation.
We meet on the last Monday of the month from 4pm-5pm PST.
Organizers: Jonathan Nelson (jnelson4@usc.edu)
Click here to join USC-SCORE and receive emails with the zoom link to attend.
| Date | Topic | Presenter | Materials |
|---|---|---|---|
| January 27th | Updates to Seurat V5 | Jonathan Nelson | SCORE #1 |
| February 24th | Advances in scRNASeq Technologies | Jeremiah Reyes | SCORE #2 |
| March 31st | Best Practices for Reporting Data (GitHub/GEO) | Jessica Bahena-Lopez | SCORE #3 |
| April 28th | Cell-Cell Interactions with CellChat | Kevin Burfeind | |
| May 26th | Access to KPMP Datasets | Xiao-Tong Su | |
| June 30th | Spatial Transcriptomic Analysis | TBD |
This session was presented by Jonathan Nelson and covers how to install R, R Studio, and Seurat, while also providing a tutorial on how to analyze a simple scRNASeq dataset of enriched glomeruli from a kidney.
Link to materials
This session was presented by Kevin Burfeind and covers how to merge two different samples into one data file and how to upload different scRNAseq file types that are commonly uploaded to GEO.
Link to materials
This session was presented by Jonathan Nelson and
Annie Lackey and covers how to use the
group.by and split.by arguments in Seurat as
well as how to generate a multi-dimensional dotplot and a 3D UMAP.
Link to materials
This session was presented by Annie Lackey and covers how to use FindIntegrationAnchors() to deal with strong batch (or disease) effects in your dataset. The example data used here was for the distal nephron of the kidney responding to ischemic injury.
Link to materials
This session was presented by Adam Munhall and covers how to work with data files and dataframes in R and was unironicallyed titled “Don’t let your data.frame you in”.
Link to materials
This session was presented by Xiao-Tong Su and Jonathan Nelson covers how to re-create from Seurat Objects different manuscript figures, including a stacked violin plot and proportion barplot.
Link to materials
This session was presented by Grace Deitzler, who at the time was a PhD candidate at Oregon State University, and covers how to create custom color palttes, creating animalted plots, and playing around with custom themes.
Link to materials
This session was presented by Xiao-Tong SU and Jeremiah Reyes, and covers how to approach a Pseudobulk analysis using DEseq2 (XTS) and GSEA (JVR) using the Cluster Profiler package.
Link to materials
This session was presented by Katie Emberley, PhD Candidate in the Emery Lab, and covers how to remove ambient RNA (with SoupX), remove doublets (doubletfinder), and integrate multiple samples together into a single object and then subset into distict populations for future analysis.
Link to materials
This session was presented by 10X Genomics and covered a preprint that showed early data using a Xenium 313-plex on FFPE tissue.
Link to materials
This session was presented by Biolegend and covered how to use CITE-seq to facilitate multi-Omic analysis of single cells.
Link to materials
This session was presented by Jonathan Nelson and covered how to use Cell Ranger starting with a Linux installation on a PC, and then how to use Shiny Cell to create an interactive web application of an scRNAseq dataset.
Link to materials
This session was presented by Greg Duncan, postdoc in the Emery Lab, and Jonathan Nelson and covered thier practical experience isolating nuclei (from Kidney, Retina, and Optic Nerve) and then enriching for specific populations using Fluorescence Activated Nuclei Sorting (FANS).
Link to materials
This session was presented by Arjun Lakshmanan and Joe Yang, high school bioinformatics interns in the Division of Nephrology at OHSU, and and covered their experiences using ChatGPT to accelerate their scRNAseq learning and analysis.
Link to materials