This workshop will cover processing single-cell RNA-seq data using the HSLS-licensed PartekFlow software. Participants will learn how to
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.
Other useful Vidoes
|PCA explained (StatQuest)||t-SNE explained (StatQuest)|
|A Guide to scRNA-Seq Normalization - BioTouring||The Why, When and How of 3D PCA - BioTouring|
|scRNA-Seq Cell Type Annotation: Common Approaches and Tools - BioTouring||The Essence of scRNA-Seq Clustering: Why and How to Do it Right|
|BioRender - Scientific illustrations creating tool||
Garnett - a tool for automated cell type classification
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
Azimuth - a tool for rapid mapping of query datasets to references
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
A hitchhiker’s guide to single-cell transcriptomics and data analysis pipelines. Genomics
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.
Please evaluate the workshop
scRNA-seq data analysis using PartekFlow