LandSCENT-package: Landscape Single Cell Entropy
In ChenWeiyan/LandSCENT: Landscape Single Cell Entropy

Description Details Author(s) References Examples

LandSCENT (Landscape Single Cell Entropy) is a R-package for the analysis of single-cell RNA-Seq data. One important feature of this package is the computation of signaling entropy, which allows single cells to be ordered according to differentiation potency. LandSCENT also integrates cell density with potency distribution to dissect cell types across all potency states and generates high-quality figures to show this.

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LandSCENT will be of interest to those analysing single-cell RNA-Sequencing data. A core component of LandSCENT is the computation of signaling entropy at the single-cell level (CompSRana), allowing cells to be ordered according to differentiation potency or phenotypic plasticity. It also incorporates functionality for quantifying intercellular heterogeneity, for identifying interesting subpopulations of cells that differ in terms of potency or plasticity, as well as to infer dependencies between single cell clusters, which for instance can help identify lineage trajectories.

Weiyan Chen & Andrew E Teschendorff

Teschendorff AE, Tariq Enver. Single-cell entropy for accurate estimation of differentiation potency from a cell’s transcriptome. Nature communications 8 (2017): 15599. doi: 10.1038/ncomms15599.

Teschendorff AE, Banerji CR, Severini S, Kuehn R, Sollich P. Increased signaling entropy in cancer requires the scale-free property of protein interaction networks. Scientific reports 5 (2015): 9646. doi: 10.1038/srep09646.

Banerji, Christopher RS, et al. Intra-tumour signalling entropy determines clinical outcome in breast and lung cancer. PLoS computational biology 11.3 (2015): e1004115. doi: 10.1371/journal.pcbi.1004115.

Teschendorff, Andrew E., Peter Sollich, and Reimer Kuehn. Signalling entropy: A novel network-theoretical framework for systems analysis and interpretation of functional omic data. Methods 67.3 (2014): 282-293. doi: 10.1016/j.ymeth.2014.03.013.

Banerji, Christopher RS, et al. Cellular network entropy as the energy potential in Waddington's differentiation landscape. Scientific reports 3 (2013): 3039. doi: 10.1038/srep03039.