scOrange Blog
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Categories:
- clustering
- t-sne
- marker-genes
- tsne
- annotator
- data-mining
- embedding
- embryo
- genomics
- markers
Author: Iva Černoša, Mar 29, 2019
Clustering Cells in Mouse Pancreas
To reproduce a part of a study by Baron et al. (Cell Systems, 2016), we cluster mouse pancreatic cells and identify marker genes for each type of the cells.
Author: Martin Stražar, Nov 23, 2018
Exploring the Fruit Fly Olfactory System
Explore different subsets of cells and related them to known biological processes.
Author: 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.
Author: Ajda Pretnar, Oct 3, 2018
Exploring cell populations with t-SNE
Single-cell RNA sequencing protocols enable measuring the transcriptome on a single-cell resolution. We explore the different cell types in a blood sample by a integrating existing knowledge on known marker genes and a t-SNE visualization, focusing on interactive exploration of data.
