For better experience, turn on JavaScript!

SpatialDE
Home » Tools » RNA-seq Tools and Software » RNA-seq core analysis » SpatialDE

SpatialDE

SpatialDE is a tool to identify spatially variable genes in data from multiplexed imaging or RNA-seq data. The SpatialDE algorithm can cluster genes for expression-based tissue histology.



SpatialDE

SpatialDE is a tool to identify spatially variable genes in data from multiplexed imaging or RNA-seq data. The SpatialDE algorithm can cluster genes for expression-based tissue histology.

Topic

Gene expression; Statistics and probability; RNA-seq; Data mining

Details

  • Operation: Statistical modelling; Expression data visualisation; Network simulation; Gene expression profiling
  • Software interface: Command-line user interface
  • Language: R, Python
  • Operating system: Linux; Mac OS X; Microsoft Windows
  • License: The MIT licence
    • Cost: Free
  • Version name: 0.1.0
  • Credit: The European Molecular Biology Laboratory (EMBL), the Wellcome Trust, ERC Consolidator Grant ThDEFINE, the EU.
  • Contact: Valentine Svensson vale _at_ ebi.ac.uk | Oliver Stegle oliver.stegle _at_ ebi.ac.uk,
  • Collection: -

Publications

Svensson V, Teichmann SA, Stegle O "SpatialDE: identification of spatially variable genes." Nat. Methods 2018; 15(5):343-346 https://doi.org/10.1038/nmeth.4636
PMID: 29553579
PMCID: PMC6350895


Download and documentation







If you find errors, please report here.

SECTIONS

Tutorials
In-house software
Blog
News
Find Jobs
History
Definition of Bioinformatics
ENCYCLOPEDIA
COVID-19
⚬ Timeline of outbreak
⚬ Blog
⚬ Scientific Facts
⚬ Daily statistics
⚬ News


TOOLS


1. SNP Tools
2. GWAS Tools
3. Genotype Imputation Tools
4. MSA tools
5. CNV tools
6. WGA tools
7. RNA-seq tools
8. Proteomics Tools
9. Nucleic Acid Structure Analysis Tools
10. Nucleic Acid Sequence Analysis Tools
11. Sequence Logo Tools
12. In-house Software Tools

Find thousands of Bioinformatics and Life Science software tools and databases in the newly launched




Ads