Click here for the single cell core sample submission form.

The Single Cell Core will be closed on Monday, September 5, according to the University approved Labor Day holiday.

Workshops and Training

10X single cell techniques

Monday, June 27, 2022; 11am-1pm

This workshop will illustrate the technological basis of 10x genomics single cell analysis. I will also introduce several chemistries 10X has developed for applications beyond single cell RNA-Seq and the sequencing read architecture of each application.

Register at: Summer 2022 NGS Workshops Registration

scRNASeq data analysis using Seurat

Tuesday, June 28, 2022; 11am-1pm

This workshop will briefly review the cellranger pipelines to process raw reads into expression values. The hands-on training will include reading the count data in R, quality control, normalization, dimensionality reduction, cell clustering, and finding marker genes. The Seurat pipeline will be covered. It also includes the integrative analysis of simulated vs control data using the anchoring framework in Seurat V3. Presented by Dhivyaa Rajasundaram.

Register at: Summer 2022 NGS Workshops Registration

Single-Cell Analysis with Bioconductor

Wednesday, June 29, 2022; 11am-1pm

This workshop will teach how to perform scRNAseq analysis using Bioconductor. The training will include many aspects of analysis such as normalization, cell type annotation of clusters, and pseudo-bulk differential gene expression. Similarities and differences to the Seurat pipeline will be mentioned.

Register at: Summer 2022 NGS Workshops Registration

Advanced Single-Cell Analysis

Thursday, June 29, 2022; 11am-1pm

This advanced workshop will focus on the analysis of multi-omics data and its integration (e.g. CITE-seq, multiome, and DOGMA-seq). The hands-on training will include background introduction and a step-by-step R pipeline with real applications from immunology.

Register at: Summer 2022 NGS Workshops Registration

Deep learning for scRNASeq analysis

Friday, July 1, 2022; 11am-1pm

This workshop will review the deep learning algorithms (variational autoencoder, autoencoder, generative adversarial network and supervised DL models ) and their applicability in the single cell RNA-seq processing pipeline. The hands-on training will provide examples to run deep learning RNASeq algorithms.

Register at: Summer 2022 NGS Workshops Registration

Center for Research Computing Workshops

The University of Pittsburgh Center for Research Computing (Pitt CRC) plays a vital role in advancing leading-edge research. The CRC, formerly the Center for Simulation and Modeling, is singularly focused on increasing the productivity of Pitt researchers through the application of advanced computing. In addition to supporting research in fields such as engineering, chemistry and genomics, Pitt CRC—a unique resource for the entire University community—now adds value to work in biostatistics, economics, and linguistics, among many other areas.
The mission of Pitt CRC is to increase the research productivity of Pitt faculty through the use of advanced computing. We fulfill this mission through outreach to the university community that includes:

  • Offering access to cutting-edge computer hardware and software for enabling transformative research.
  • Workshops teaching the most effective ways to use Pitt CRC’s computing resources.
  • Personalized consultation on refining projects at the computational code level — such as stronger algorithms to take advantage of parallel processing — and at the level of improving the user experience for researchers who begin taking advantage of high performance computing using a familiar graphic user interface.

Contact Us

Contact us for a free consultation regarding your next single cell experiment.