JColorGrid protocols

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Associated diseases

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JColorGrid specifications

Information


Unique identifier OMICS_26488
Name JColorGrid
Software type Application/Script
Interface Command line interface, Graphical user interface
Restrictions to use None
Output data A color-grid
Output format JPEG,EPS
Operating system Unix/Linux, Mac OS, Windows
Programming languages Java
License GNU General Public License version 2.0
Computer skills Advanced
Version 1.861
Stability Stable
Maintained Yes

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Maintainer


  • person_outline Marcin Joachimiak <>

Publication for JColorGrid

JColorGrid in pipeline

2012
PMCID: 3429548
PMID: 22562043
DOI: 10.4161/auto.20069

[…] most genes are represented by multiple 60-mer oligos on the whole-genome microarray, all p < 0.05 fold change values were collected for each gene of interest, averaged, and then visualized using jcolorgrid for the expression analysis of individual atg genes. blastp searches were used to find homologous gene products in yeast, drosophila and human, and the top-scoring hit is shown […]


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JColorGrid in publications

 (13)
PMCID: 5758752
PMID: 29311626
DOI: 10.1038/s41598-017-17944-4

[…] as μg of target protein/mg of tissue total protein. normalized cytokine or chemokine concentrations were transformed to their log10 values and the averaged data used to generate a heat map with jcolorgrid software., whole epididymides from saline-control, lps- and lta-treated rats were immersed in bouin’s fixative (75 ml saturated picric acid, 5 ml glacial acetic acid, 25 ml 37% […]

PMCID: 5718816
PMID: 28933684
DOI: 10.1080/21645515.2017.1380137

[…] gp120 matching current circulating hiv-1 isolates, including clade a1, a2, b, c, d, e, f1, f2, g, h, ag, ab, bc, cd, bf and bg, were determined. the heatmap of coverage percentage was constructed by jcolorgrid software with input gp120 protein sequences., to analyze the statistical significance of antibody responses induced by different vaccination regimens, one way anova, t-test and fisher […]

PMCID: 5451456
PMID: 28566699
DOI: 10.1038/s41598-017-02656-6

[…] using the vegdist function. significance tests were based on 1000 permutations for all performed analyses., the relative otu abundance and distribution on phylum level was plotted as heatmap using jcolorgrid. hierarchical clustering of otus (relative abundance & presence/absence) and rank-specific datasets were performed using vegdist (bray-curtis) and hclust (method = ‘average’). […]

PMCID: 5118433
PMID: 27921008
DOI: 10.3389/fcimb.2016.00154

[…] inc., cary, nc). shared otus among gut sites at different age were plotted as venn diagrams using the r environment (package “venndiagram,” version 1.6.17.) (chen, ). heatmaps were created using jcolorgrid (joachimiak et al., )., statistically significant differences in relative abundance with regard to sampling sites and time were calculated using “metastats” in mothur, which is based […]

PMCID: 4777738
PMID: 26973642
DOI: 10.3389/fmicb.2016.00274

[…] of the nonparametric species richness estimators chao 1 and ace, the diversity indices shannon, simpson and shannoneven, the “summary.single” command was used. heatmaps were created using jcolorgrid (joachimiak et al., ). for bray-curtis analysis, explicet version 2.10.15 (robertson et al., ) was applied. the 50 most abundant otus of all sampling time points were additionally […]


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JColorGrid institution(s)
Department of Plant and Microbial Biology, University of California Berkeley, CA, USA; Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, CA, USA; Institute for Neurodegenerative Diseases and Department of Neurology, University of California San Francisco, San Francisco, CA, USA
JColorGrid funding source(s)
Supported by NIH/NIGMS P20 GM068136 and NIH/NHGRI K22 HG00056, The Giannini Family Foundation, NIH/NIAID U01 AI53862 and by NIA P01 AG021601.

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