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HSLS MolBio Workshops

Information & resources for hands-on bioinformatics classes.

Workshop description

Register and join our comprehensive Workshop Series: Mastering Single-Cell Analysis with Partek Flow to gain a deep understanding of single cell data analysis. This four-part series, leveraging Partek Flow software, will cover the entire workflow, from data import, pre processing to results interpretation and visualization.

Register for Workshop 1: Introduction to Single Cell Technologies and Partek Flow

Explore the fundamentals of single cell technologies and Partek Flow software. Learn how to seamlessly transition from Fastq to single cell countmatrix using 10x Cloud and Partek flow.

Register for Workshop 2: Basic ScRNASeq Analysis Using Partek Flow

Dive into basic ScRNASeq analysis using Partek Flow, focusing on one sample dataset. Gain hands-on experience with data analysis workflows and visualization.

Register for Workshop 3: Advanced ScRNASeq Analysis Using Partek Flow

Delve into advanced ScRNASeq analysis techniques using Partek Flow, exploring multiple sample datasets. Enhance your skills in complex single cell rnaseq data analysis covering advanced options such as batch effects correction methods, and visualization techniques.

Register for Workshop 4: Single Cell Multiomics Analysis Using Partek Flow

Discover the power of single cell multiomics analysis using Partek Flow, covering CITESeq, ScATACSeq, and more. Integrate multiple data types for comprehensive insights.

Objectives

Upon completing this series, you should be able to

  • Describe single cell technologies and data analysis pipelines
  • Use Partek Flow software for analyzing and visualizing single cell data
  • Perform single cell transcriptomic analysis and visualization 
  • Integrate single cell transcriptomics data with other omics data such as proteomics and epigenomic data

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 no programming expereince is required.

Workshop Materials

Workshop 1Introduction to Single Cell Technologies, 10X Genomics and Partek Flow
Workshop 2 : Basic ScRNASeq Analysis Using Partek Flow
  • Datasets and PowerPoint: Workshop 2 Matrials
  • Lecture Video: scRNA seq data analysis with single sample 
Workshop 3 : Advanced ScRNASeq Analysis Using Partek Flow
  • Datasets and Powerpoint: Workshop 3 Materials
  • Lecture Video: scRNA seq data analysis with Multiple samples 
Workshop 4: Single Cell Multiomics Analysis Using Partek Flow

Software Registration

HSLS Software Registration for PartekFlow

Databases and Tools

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

CellMarker database : CellMarker 2.0: an updated database of manually curated cell markers in human/mouse and web tools based on scRNA-seq data

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

PangloDB : A database for the scientific community interested in exploration of single cell RNA sequencing experiments from mouse and human

Annotation of cell types (ACT): A convenient web server for cell type annotation

Attribution

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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