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HSLS MolBio Workshops

Information & resources for hands-on bioinformatics classes.


This workshop will cover processing single-cell RNA-seq data using the HSLS-licensed PartekFlow software. Participants will learn how to  

  • import FASTQ/Count matrix files from scRNA-Seq experiments to PartekFlow software
  • perform quality checks (QC) on single-cell data 
  • filter and normalize the data 
  • generate PCA and t-SNE plots to visualize data 
  • identify cell populations, and biomarkers 
  • compute differential gene expressions between two cell populations and/or multiple samples 

Target Audience

Experimental biologists seeking to analyze scRNA-Seq 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

Data Download

Software Registration

Useful Resources

BioRender - Scientific illustrations creating tool

Garnett - a tool for automated cell type classification

Introduction to single-cell RNA-seq technologies

SequenceENG: an interactive learning resource for next-generation sequencing (NGS) techniques


Awesome-single-cell - List of software packages (and the people developing these methods) for single-cell data analysis, including RNA-seq, ATAC-seq, etc.


Cell Ranger - a set of analysis pipelines that process Chromium single-cell data to align reads, generate feature-barcode matrices, perform clustering and other secondary analysis, and more

The Human Cell Atlas

Azimuth - a tool for rapid mapping of query datasets to references



Additional Resources

ScRNASeq Analysis using CLC Genomics Software :

Powerpoint :  scRNA-seq data analysis using CLC Genomics Workbench (03/29/2022)

Lecture video : Introduction to scRNA-seq data analysis using CLC Genomics Workbench (offered on 11/17/2021) (3 hrs)

Additional Datasets :

GSE161267 (MEX); A single-cell atlas of human teeth

CLC Genomics Webinar