Introducing a New Tool for Single-Cell Gene Expression Analysis

Are you ever in need of easy-to-use, robust tools and algorithms to help analyze, annotate, and identify cell types in your single-cell NGS data? Do you ever want to discover key biomarkers for cell types, tissues, and diseases without the tedious work of curating and analyzing each dataset? Do you ever look for the biological context of specific pathways underlying your single-cell data?

HSLS Molecular Biology Information Service is pleased to announce that we now license three concurrent seats for a new single-cell gene expression analysis module within the long-licensed CLC Genomics Workbench from QIAGEN Digital Insights. It is point-and-click, GUI-based software that does not require programming experience to use. Uncover new and unexpected biological discoveries from individual cells via these key applications:

  • scRNA-seq for biomarker discovery—perform single-cell data analysis from raw FASTQ files to clusters of cells with annotated cell types and differentially expressed genes
  • Visualization of scRNA-seq data—create interactive 2D and 3D visualizations of UMAP and tSNE plots for single-cell expression data overlaid with cluster information, cell annotations, and gene expressions
  • Cross comparison of scRNA-seq data—discover subtle differences in gene expression among individual cells by importing and processing single-cell experiments, starting with raw FASTQ or quantification data using an scRNA-seq pipeline
  • Annotation of cell types—annotate individual cells using a cell classifier and differential gene expression for GO analysis to guide additional manual cluster annotation
  • Single-cell pathway analysis—upload differential gene expression results into HSLS-licensed Ingenuity Pathway Analysis to gain deeper insight into the biological mechanism driving expression differences

Researchers with a Pitt or UPMC email address may register for access to CLC Genomics Workbench software, which is required to install a plugin for the CLC single-cell gene expression analysis module. Numerous resources are available to get you started using the tool:

Contact the HSLS Molecular Biology Information Service with any questions or to schedule a consultation about this valuable new tool for single-cell gene expression analysis.

~Carrie Iwema