Matrix2png protocols

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Matrix2png specifications

Information


Unique identifier OMICS_25517
Name Matrix2png
Interface Web user interface
Restrictions to use None
Input data A single tab-delimited text file containing numerical values in a simple ‘spreadsheet’ format.
Input format TSV
Output format PNG
Programming languages C
Computer skills Basic
Version 1.2.1
Stability Stable
Maintained Yes

Maintainers


  • person_outline Paul Pavlidis <>
  • person_outline Paul Pavlidis <>

Additional information


https://matrix2png.msl.ubc.ca/bin/matrix2png.cgi https://matrix2png.msl.ubc.ca/matrix2image.html

Information


Unique identifier OMICS_25517
Name Matrix2png
Software type Application/Script
Interface Command line interface
Restrictions to use None
Input data A single tab-delimited text file containing numerical values in a simple ‘spreadsheet’ format.
Input format TSV
Output format PNG
Operating system Unix/Linux, Windows
Programming languages C
Computer skills Advanced
Version 1.2.1
Stability Stable
Maintained Yes

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Maintainers


  • person_outline Paul Pavlidis <>
  • person_outline Paul Pavlidis <>

Additional information


https://matrix2png.msl.ubc.ca/bin/matrix2png.cgi https://matrix2png.msl.ubc.ca/matrix2image.html

Publication for Matrix2png

Matrix2png in pipelines

 (2)
2014
PMCID: 4274413
PMID: 24936762
DOI: 10.1038/ismej.2014.101

[…] treatment comparison, under implementation of the alexa's algorithm ()., heat maps of normalized expression of genes common to specific comparison sets were produced by using the web-based program matrix2png (). thresholded and 2log transformed expression data from genespring were used as input in matrix2png under the parameters: normalize rows and preset map 17. the average of the expression […]

2011
PMCID: 3093658
PMID: 21562564
DOI: 10.1038/nature09999

[…] using the previously published robust multi-array average (rma) algorithm using the genespring gx software (agilent, palo alto, ca). the gene expression intensity presentations were generated with matrix2png software (http://chibi.ubc.ca/matrix2png/bin/matrix2png.cgi) or multi experiment viewer software (http://www.tm4.org/mev/)., geneset enrichment analysis was performed using gsea software […]


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Matrix2png in publications

 (97)
PMCID: 5915532
PMID: 29691398
DOI: 10.1038/s41467-018-04063-5

[…] genbank accession numbers were mapped to the ingenuity database (ipa, http://www.ingenuity.com) to retrieve relevant biological processes. heat maps were generated using the web interface programme matrix2png., all data are expressed as mean ± s.e.m. replicates were biological replicates and n represents the number of individual mice analysed per experiment. mice were assigned to groups […]

PMCID: 5870378
PMID: 29587643
DOI: 10.1186/s12870-018-1261-1

[…] differences in the profile composition. nmds ordinations and associated anosim tests were run for each digestive enzyme. visualization of the relative abundance using heatmaps was done using matrix2png interface (http://www.chibi.ubc.ca/matrix2png/bin/matrix2png.cgi)., six rice cultivars grown under normal soil conditions at the experimental fields of rda (south korea) were selected […]

PMCID: 5864832
PMID: 29568061
DOI: 10.1038/s41467-018-03523-2

[…] exact test). hierarchical cluster was performed by centered correlation (both baits and interactors; average linkage) using cluster 3.0 and the clusters were visualized with tree view 1.1.6 and the matrix2png web server (http://www.chibi.ubc.ca/matrix2png/)., protein interaction networks are constructed from saint data that were imported into cytoscape 3.2.1. the known prey-prey interaction […]

PMCID: 5916252
PMID: 29467331
DOI: 10.1172/jci.insight.97228

[…] mean and normalized centering of the gene expression levels. clustering was completed using centered correlation metric and complete linkage. heat maps were generated using java treeview 1.1.6r4 and matrix2png 1.2.1. the yellow, black, and blue color scale in represents the respective expression level of a gene above, equal to, or below the mean expression for that gene across all samples. gene […]

PMCID: 5771609
PMID: 29342173
DOI: 10.1371/journal.pone.0191201

[…] for pathways analysis to link genomic information with higher order functional information. for preparation of heat maps of some important differentially expressed genes, a web based application matrix2png was used []. for making interacting network of genes, string database tool was used []., quantitative rt-pcr (qrt-pcr) amplifications were performed in additional sets of sc cultures […]


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Matrix2png institution(s)
Columbia Genome Center, Columbia University, New York, NY, USA; Department of Genome Sciences, University of Washington, Seattle, WA, USA

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