Orange3-SingleCell 1.4.0

Add-on for bioinformatics analysis of single cell data.

Orange3 Single Cell

The Single Cell add-on for Orange3 adds functionality for analysis of single cell data. The widgets enable gene filtering, preprocessing, batch effect removal, gene and cell scoring and cluster analysis. The widgets can be used seamlessly with other Orange widgets, including those from Orange3-Bioinformatics add-on.

Features

Explore the Diversity of Cells

• load data from any platform and filter outlier cells
• normalize expression values across samples and platforms
• identify and explore sub-populations with a sample and across multiple samples

Discover New Marker Genes

• identify signature genes for each subpopulation using multiple methods
• use gene ontology enrichment to explore the biological meaning and identify cell types

Predict New Cell Types

• build classifiers to identify the cell type of each subpopulation
• use classifier on new data samples to predict cell types and focus on interesting cell type populations