TreeView pipeline

TreeView specifications

Information


Unique identifier OMICS_01574
Name TreeView
Alternative names Java Treeview, JavaTreeView
Software type Package/Module
Interface Command line interface, Graphical user interface
Restrictions to use None
Operating system Unix/Linux, Mac OS, Windows
Programming languages Java
License GNU General Public License version 2.0
Computer skills Medium
Version 1.1.6
Stability Stable
Maintained Yes

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Maintainer


  • person_outline Alok Saldanha <>

Publications for TreeView

library_books

Java Treeview—extensible visualization of microarray data.

2004 Bioinformatics
DOI: 10.1093/bioinformatics/bth349

TreeView IN pipelines

 (8)
2012
PMCID: 3392818
PMID: 22300536
DOI: 10.1186/ar3707

[…] and average linkage, with the mfi value of undetected array features set to 0 and with positive control samples excluded from being weighted in the clustering process. results were displayed using java treeview software [49]. significance of overlap between mouse igm and igg autoantigen reactivity was determined using cumulative hypergeometric distribution with a total population size of 122 […]

2012
PMCID: 3392818
PMID: 22300536
DOI: 10.1186/ar3707

[…] average linkage, with the mfi value of undetected array features set to 0 and with positive control samples excluded from being weighted in the clustering process. results were displayed using java treeview software [49]. significance of overlap between mouse igm and igg autoantigen reactivity was determined using cumulative hypergeometric distribution with a total population size of 122 […]

2012
PMCID: 3538056
PMID: 23210427
DOI: 10.1186/1755-8794-5-58

[…] (fdr) [11]. hierarchical clustering was performed using gene cluster 3.0 using mean-centered expression data in a complete linkage, correlation-based approach [12]; clusters were visualized using java treeview [13]. the cell-type specificity of gene expression was evaluated using whole-blood normalized expression values derived from biogps [14]., genes for qrt-pcr were selected […]

2012
PMCID: 3538056
PMID: 23210427
DOI: 10.1186/1755-8794-5-58

[…] [11]. hierarchical clustering was performed using gene cluster 3.0 using mean-centered expression data in a complete linkage, correlation-based approach [12]; clusters were visualized using java treeview [13]. the cell-type specificity of gene expression was evaluated using whole-blood normalized expression values derived from biogps [14]., genes for qrt-pcr were selected from the microarray […]

2012
PMCID: 3546428
PMID: 23151021
DOI: 10.1186/1471-2164-13-619

[…] and 10,000 bootstrap iterations were performed to assess the significance of the observed the stability of the clusters using the pvclust package for r [60]. resulting clusters were visualised with java treeview [61]. two strategies were applied for gene expression signature analysis: (1) when centroids for specific classes (e.g. bc subtypes or groups of er-negative breast tumours [25]) […]

TreeView institution(s)
Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA
TreeView funding source(s)
Supported by a National Defense Science and Engineering Graduate Fellowship, the Stanford Genome Training Program (Training Grant NIH 5 T32 HG00044) and NIH grants HG 01315 and GM 46406.

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