Embeddr specifications


Unique identifier OMICS_10060
Name Embeddr
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux, Mac OS, Windows
Programming languages R
License GNU General Public License version 3.0
Computer skills Advanced
Version 0.99.0
Stability Stable
Maintained Yes




No version available



  • person_outline kieran.campbell

Publication for Embeddr

Embeddr citation


Single Cell Transcriptomics Bioinformatics and Computational Challenges

Front Genet
PMCID: 5030210
PMID: 27708664
DOI: 10.3389/fgene.2016.00163

[…] o Waterfall, TSCAN is a new approach based on MST. Cells are first clustered using a model-based approach before constructing an MST, allowing the reduction of the tree space complexity (Ji and Ji, ).Embeddr is a method that uses the correlation metric between cells to construct kNNG, then projects the samples into a low-dimensional embedding using Laplacian eigen maps. The pseudo time order is th […]

Embeddr institution(s)
MRC Functional Genomics Unit, University of Oxford, UK
Embeddr funding source(s)
Supported by the UK Medical Research Council.

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