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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 Video

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

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