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Tools for Single Cell ANalysis TSCAN

A software tool developed to better support in silico pseudo-time reconstruction in single-cell RNA-seq analysis. TSCAN uses a cluster-based minimum spanning tree (MST) approach to order cells. Cells are first grouped into clusters and an MST is then constructed to connect cluster centers. Pseudo-time is obtained by projecting each cell onto the tree, and the ordered sequence of cells can be used to study dynamic changes of gene expression along the pseudo-time. Clustering cells before MST construction reduces the complexity of the tree space. This often leads to improved cell ordering. It also allows users to conveniently adjust the ordering based on prior knowledge. TSCAN has a graphical user interface (GUI) to support data visualization and user interaction. Furthermore, quantitative measures are developed to objectively evaluate and compare different pseudo-time reconstruction methods.

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TSCAN forum

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TSCAN classification

TSCAN specifications

Interface:
Web user interface
Computer skills:
Basic
Maintained:
Yes
Restrictions to use:
None
Stability:
Stable

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TSCAN classification

TSCAN specifications

Software type:
Package/Module
Restrictions to use:
None
Programming languages:
R
Computer skills:
Advanced
Stability:
Stable
Interface:
Command line interface, Graphical user interface
Operating system:
Unix/Linux, Mac OS, Windows
License:
GNU General Public License version 3.0
Version:
1.10.2
Maintained:
Yes

TSCAN distribution

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TSCAN support

Documentation

Maintainer

  • Hongkai Ji <>
  • Hongkai Ji <>

Credits

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Publications

Institution(s)

Department of Biostatistics, Johns Hopkins University Bloomberg School of Public Health, Baltimore, MD, USA

Funding source(s)

National Institutes of Health (NIH) [R01HG006282]

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