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HSLS MolBio Workshops

Information & resources for hands-on bioinformatics classes.


This workshop is focused on Single cell multiomics data analysis - CITE-Seq and Single Cell ATAC+Gene expression. While CITE Seq enables researchers to capture both RNA and protein expression simultaneously, the Sc ATAC+Gene expresion method allows researchers to measure both chromatin accessibility and mRNA expression at the same time.

Participants will learn how to

  • import 10x Genomics CITE-Seq/Sc ATAC+Gene expression data into PartekFlow
  • check the quality of the data
  • filter and normalize the data
  • generate UMAP plots to visualize data
  • identify cell populations and biomarkers using multiome data and visualize 

Target Audience

Experimental biologists seeking to analyze single cell sequencing data generated through experiments or retrieved from a repository such as GEO. The software covered in the workshop operates through a user-friendly, point-and-click graphical user interface, so neither programming experience nor familiarity with the command line interface is required.

Workshop Materials

Software Registration


Data Download (10x Genomics)

Tutorials and Webinars

Databases and Tools


  • Cell Marker - a manually curated resource of cell markers in human and mouse
  • Panglao db - a database for single cell RNA seq experiments from mouse and human
  • The Human Cell Atlas and The Human Protein Atlasthe expression profiles in single-cell types
  • scRNASeqDB -  a database for gene expression profiling in human single cell by RNA-seq
  • Single Cell Expression Atlas - single cell gene expression data across species
  • Single Cell Portal (Broad Institute) -  portal that contains an analysis of human glioma, immune, and other stromal cells at the single cell level
  • Tabula Muris - a compendium of single cell transcriptome data from Mus musculus
  • Tabula Sapiens - a compendium of single cell transcriptome data from Homo sapiens
  • Cellstar - The comprehensive database of single-cell transcriptomics annotation resources from multiple organisms


  • Cell Ranger  - a set of 10x genomics analysis pipelines that process chromium data
  • Azimuth - a tool for rapid mapping of query datasets to references
  • Garnett - a tool for automated cell type classification
  • ACT -  Annotation of cell types (ACT): a convenient web server for cell type annotation
  • SingleR - Using SingleR to annotate single-cell RNA-seq data
  • GPTCelltype - GPT-4 for cell type annotation in single-cell RNA-seq analysis 



Please include the following statement in the acknowledgments section for all publications, posters, and presentations:

[software name, such as Partek Flow ] software licensed through the Molecular Biology Information Service of the Health Sciences Library System, University of Pittsburgh (RRID:SCR_011975) was used for data analysis.

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