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HSLS MolBio Workshops

Information & resources for hands-on bioinformatics classes.

Objective

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

Partek flow

PowerPoints

Lecture Videos

Data Download

  • scRNA-Seq -

Software Registration

Useful Resources

scRNA-seq best practices- a digital book which aims to teach common workflows for the analysis of single-cell RNA-Seq 

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

SEQanswers

Biostars 

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

References

Attribution

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

[software name, such as CLC Genomics workbench, 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.