scOrange Blog

By: Martin Stražar, Nov 23, 2018

Exploring the Fruit Fly Olfactory System

Explore different subsets of cells and related them to known biological processes.

By: Martin Stražar, Oct 23, 2018

scOrange representing the FAIR principles in bioinformatics

scOrange's away trip to Genova.

By: Martin Stražar, Oct 5, 2018

Nuts and bolts: Preprocessing and Removing Batch Effects

Preprocess raw read count data to make expression values comparable across cells and genes. Use Gene Markers and Score Cells to estimate the cell cycle phase of each cell and regress out this confouding factor.

By: Ajda Pretnar, Oct 4, 2018

Cell Clustering and Cluster Analysis

Discovering new marker genes is a core step in the analysis of single-cell sequencing data. Use Louvain clustering to find cell populations and visualize the cell landscape in a t-SNE projection. Examine the contents of each cluster by finding differentially expressed genes and their related functions according to the Gene Ontology database.