SCExV: a webtool for the analysis and visualisation of single cell qRT-PCR data

Area of Science:

• Molecular Biology
• Genomics
• Immunology

Background:

• Single-cell gene expression assays are crucial for analyzing heterogeneous cell populations.
• Existing tools often lack a unified, user-friendly interface for both analysis and visualization.
• There is a need for accessible solutions for researchers without extensive bioinformatics expertise.

Purpose of the Study:

• To develop an intuitive webtool for the analysis and visualization of single-cell gene expression data.
• To provide a unified platform that combines data analysis and visualization capabilities.
• To accommodate users with varying levels of bioinformatics proficiency.

Main Methods:

• Developed the Single cell expression visualiser (SCExV) webtool.
• Enabled direct input of Ct value data matrices, including those from Fluidigm Biomark.
• Integrated cell surface marker intensity data from index sorting.

Main Results:

• SCExV expedites the analysis of single-cell qRT-PCR data.
• The tool visualizes relationships between gene expression profiles and cell immunophenotype.
• Handles diverse data inputs, including Ct values and marker intensities.

Conclusions:

• SCExV is a freely available webtool for importing, filtering, analyzing, and visualizing single-cell gene expression data.
• The tool allows simultaneous consideration of gene expression and cellular immunophenotype.
• SCExV offers an intuitive user experience with advanced functionality and analytical flexibility.