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JColorGrid specifications


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




No version available


  • person_outline Marcin Joachimiak

Publication for JColorGrid

JColorGrid citations


Lipopolysaccharide and lipotheicoic acid differentially modulate epididymal cytokine and chemokine profiles and sperm parameters in experimental acute epididymitis

Sci Rep
PMCID: 5758752
PMID: 29311626
DOI: 10.1038/s41598-017-17944-4

[…] essed 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. […]


Screening of primary gp120 immunogens to formulate the next generation polyvalent DNA prime protein boost HIV 1 vaccines

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. […]


Host specific assembly of sponge associated prokaryotes at high taxonomic ranks

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

[…] ated 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’). In addition t […]


Age Related Differences in the Luminal and Mucosa Associated Gut Microbiome of Broiler Chickens and Shifts Associated with Campylobacter jejuni Infection

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

[…] tute 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., ). […]


Epimural Indicator Phylotypes of Transiently Induced Subacute Ruminal Acidosis in Dairy Cattle

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

[…] calculation 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 classifie […]


In four shallow and mesophotic tropical reef sponges from Guam the microbial community largely depends on host identity

PMCID: 4841226
PMID: 27114882
DOI: 10.7717/peerj.1936
call_split See protocol

[…] using the vegan function simper for similarity percentages (SIMPER). Relative abundance of the 30 most abundant OTUs (each ≥0.5% relative abundance) and relative phylum abundance were visualized with JColorGrid (). Representative sequences of the 30 most abundant OTUs were assembled via the get.oturep command in mothur and BLAST searched against the NCBI Nucleotide collection (discontiguous megabl […]

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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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