HeatMapViewer protocols

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HeatMapViewer specifications

Information


Unique identifier OMICS_04852
Name HeatMapViewer
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux
Programming languages Javascript
Computer skills Advanced
Stability Stable
Maintained Yes

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Maintainer


  • person_outline Guy Yachdav <>

Publication for HeatMapViewer

HeatMapViewer in pipelines

 (2)
2016
PMCID: 5398402
PMID: 27456940
DOI: 10.4143/crt.2016.106

[…] (fdrs) were calculated using three genepattern software modules (http://www.broadinstitute.org/cancer/software/genepattern; comparativemarkerselection ver. 10, hierarchicalclustering ver. 6, and heatmapviewer ver. 13) []. the cutoff value for fdr significance was < 0.05. the significantly regulated genes were subjected to functional gene classification using the david bioinformatics […]

2014
PMCID: 4252108
PMID: 25460179
DOI: 10.1371/journal.pone.0114491

[…] version 2.3.25) . bee swarm and box plots were created using the beeswarm package in the cran repository (http://cran.r-project.org/). heat map views of gene expression data were displayed using heatmapviewer module in genepattern ., the somatic mutations identified in samples acquired from 34 japanese patients with hgsoc were catalogued according to the analysis of exome sequencing data. […]


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HeatMapViewer in publications

 (22)
PMCID: 5904193
PMID: 29696133
DOI: 10.3389/fonc.2018.00104

[…] statistical significance was determined using 1,000 random permutations of each gene set to obtain a nominal p-value and false discovery rate. heat map was generated using genepattern (). heatmapviewer (v11) was used to display values in heat map format for the genes identified from gsea analysis., the microarray data have been deposited into the geo database with the accession number […]

PMCID: 5620178
PMID: 28978038
DOI: 10.18632/oncotarget.18641

[…] carried out in a viia™ 7 real-time pcr system (thermo fisher scientific) []. expression values were represented as the reciprocal ct value for each target gene and plotted in a heatmap using the heatmapviewer module (version 13.9; broad institute) at the genepattern platform []. rna isolated from cells in the ctc outlet after processing the blood of healthy individuals and from a sample […]

PMCID: 5134101
PMID: 27905881
DOI: 10.1186/s12868-016-0314-3

[…] differentially expressed beadarray features corresponding to transcripts were queried for relationships using go, gather, and gsea [, ]. heatmaps of enriched transcript subsets were visualized using heatmapviewer within genepattern 3.8.0., excised drg from adult naïve rats were briefly rinsed in hbss to remove excess blood from tissue before placing in a well of 24-well plates containing drg […]

PMCID: 5398402
PMID: 27456940
DOI: 10.4143/crt.2016.106

[…] (fdrs) were calculated using three genepattern software modules (http://www.broadinstitute.org/cancer/software/genepattern; comparativemarkerselection ver. 10, hierarchicalclustering ver. 6, and heatmapviewer ver. 13) []. the cutoff value for fdr significance was < 0.05. the significantly regulated genes were subjected to functional gene classification using the david bioinformatics […]

PMCID: 4942931
PMID: 27406064
DOI: 10.1186/s13287-016-0351-y

[…] analyses were performed using algorithms available in the r platform (r foundation, vienna, austria) through the linear models for microarray data (limma) package []. heatmaps were generated by the heatmapviewer module of genepattern 2.0 software []. genes with p < 0.05 and fold change (fc) > 2.0 were considered differentially expressed. microarray data were deposited in the public […]


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HeatMapViewer institution(s)
TUM, Department of Informatics, Bioinformatics & Computational Biology, Garching/ Munich, Germany; TUM Graduate School of Information Science in Health (GSISH), Garching/Munich, Germany; Biosof LLC, New York, NY, USA; Bioinformatics Unit, G.S.W. Faculty of Life Sciences, Tel Aviv University, Tel Aviv, Israel

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