Scedar¶
Scedar (Single-cell exploratory data analysis for RNA-Seq) is a reliable and easy-to-use Python package for efficient visualization, imputation of gene dropouts, detection of rare transcriptomic profiles, and clustering of large-scale single cell RNA-seq (scRNA-seq) datasets.
Demo¶
Workflow of using scedar to analyze an scRNA-seq dataset with 3005 mouse
brain cells and 19,972 genes generated using the STRT-Seq UMI protocol by
Zeisel et al. (2015). Procedures and parameters that are not directly related
to data analysis are omitted. The full version of the demo is available at the
Tutorial section.
Data sources:
- Zeisel, A., Muñoz-Manchado, A. B., Codeluppi, S., Lönnerberg, P., La Manno, G., Juréus, A., Marques, S., Munguba, H., He, L., Betsholtz, C., Rolny, C., Castelo-Branco, G., Hjerling-Leffler, J., and Linnarsson, S. (2015). Cell types in the mouse cortex and hippocampus revealed by single-cell RNA-seq . Science, 347 (6226), 1138–1142.
- Hemberg Group scRNA-seq datasets