Literature DB >> 23036855

TreeVis: a MATLAB-based tool for tree visualization.

Peng Qiu1, Sylvia K Plevritis.   

Abstract

Network-based analyses of high-dimensional biological data often produce results in the form of tree structures. Generating easily interpretable layouts to visualize these tree structures is a non-trivial task. We present a new visualization algorithm to generate two-dimensional layouts for complex tree structures. Implementations in both MATLAB and R are provided.
Copyright © 2012 Elsevier Ireland Ltd. All rights reserved.

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Year:  2012        PMID： 23036855      PMCID： PMC3508366          DOI： 10.1016/j.cmpb.2012.08.008

Source DB:  PubMed          Journal:  Comput Methods Programs Biomed        ISSN： 0169-2607            Impact factor:   5.428


  8 in total

1.  Cytoscape: a software environment for integrated models of biomolecular interaction networks.

Authors:  Paul Shannon; Andrew Markiel; Owen Ozier; Nitin S Baliga; Jonathan T Wang; Daniel Ramage; Nada Amin; Benno Schwikowski; Trey Ideker
Journal:  Genome Res       Date:  2003-11       Impact factor: 9.043

2.  Single-cell mass cytometry of differential immune and drug responses across a human hematopoietic continuum.

Authors:  Sean C Bendall; Erin F Simonds; Peng Qiu; El-ad D Amir; Peter O Krutzik; Rachel Finck; Robert V Bruggner; Rachel Melamed; Angelica Trejo; Olga I Ornatsky; Robert S Balderas; Sylvia K Plevritis; Karen Sachs; Dana Pe'er; Scott D Tanner; Garry P Nolan
Journal:  Science       Date:  2011-05-06       Impact factor: 47.728

3.  Clustering gene expression data using a graph-theoretic approach: an application of minimum spanning trees.

Authors:  Ying Xu; Victor Olman; Dong Xu
Journal:  Bioinformatics       Date:  2002-04       Impact factor: 6.937

4.  Network-based inference of cancer progression from microarray data.

Authors:  Yongjin Park; Stanley Shackney; Russell Schwartz
Journal:  IEEE/ACM Trans Comput Biol Bioinform       Date:  2009 Apr-Jun       Impact factor: 3.710

5.  Discovering biological progression underlying microarray samples.

Authors:  Peng Qiu; Andrew J Gentles; Sylvia K Plevritis
Journal:  PLoS Comput Biol       Date:  2011-04-14       Impact factor: 4.475

6.  Extracting a cellular hierarchy from high-dimensional cytometry data with SPADE.

Authors:  Peng Qiu; Erin F Simonds; Sean C Bendall; Kenneth D Gibbs; Robert V Bruggner; Michael D Linderman; Karen Sachs; Garry P Nolan; Sylvia K Plevritis
Journal:  Nat Biotechnol       Date:  2011-10-02       Impact factor: 54.908

7.  Inferring phenotypic properties from single-cell characteristics.

Authors:  Peng Qiu
Journal:  PLoS One       Date:  2012-05-25       Impact factor: 3.240

8.  Identification of markers associated with global changes in DNA methylation regulation in cancers.

Authors:  Peng Qiu; Li Zhang
Journal:  BMC Bioinformatics       Date:  2012-08-24       Impact factor: 3.169
  8 in total
  3 in total

1.  Visualization and cellular hierarchy inference of single-cell data using SPADE.

Authors:  Benedict Anchang; Tom D P Hart; Sean C Bendall; Peng Qiu; Zach Bjornson; Michael Linderman; Garry P Nolan; Sylvia K Plevritis
Journal:  Nat Protoc       Date:  2016-06-16       Impact factor: 13.491

2.  Unfold High-Dimensional Clouds for Exhaustive Gating of Flow Cytometry Data.

Authors:  Peng Qiu
Journal:  IEEE/ACM Trans Comput Biol Bioinform       Date:  2014 Nov-Dec       Impact factor: 3.710

3.  The RETA Benchmark for Retinal Vascular Tree Analysis.

Authors:  Xingzheng Lyu; Li Cheng; Sanyuan Zhang
Journal:  Sci Data       Date:  2022-07-11       Impact factor: 8.501
  3 in total

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