Source Code Biol Med 2014 24;9(1):30. Epub 2014 Dec 24.
Center for Therapeutic Innovation and Department of Psychiatry and Behavioral Sciences, University of Miami Miller School of Medicine, 1120 NW 14th ST, Miami, 33136 FL USA.
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PLoS One 2017 11;12(5):e0176334. Epub 2017 May 11.
Center for Therapeutic Innovation, University of Miami Miller School of Medicine, 1501 NW 10th Ave., Miami, FL, 33136, United States of America.
Background: Transcriptomics, metabolomics, metagenomics, and other various next-generation sequencing (-omics) fields are known for their production of large datasets, especially across single-cell sequencing studies. Visualizing such big data has posed technical challenges in biology, both in terms of available computational resources as well as programming acumen. Since heatmaps are used to depict high-dimensional numerical data as a colored grid of cells, efficiency and speed have often proven to be critical considerations in the process of successfully converting data into graphics. Read More
Bioinformatics 2011 Apr 28;27(7):1009-10. Epub 2011 Jan 28.
Australian Infectious Diseases Research Centre, School of Chemistry and Molecular Biosciences, University of Queensland, Brisbane, QLD 4072, Australia.
Unlabelled: Easyfig is a Python application for creating linear comparison figures of multiple genomic loci with an easy-to-use graphical user interface. BLAST comparisons between multiple genomic regions, ranging from single genes to whole prokaryote chromosomes, can be generated, visualized and interactively coloured, enabling a rapid transition between analysis and the preparation of publication quality figures.
Availability: Easyfig is freely available (under a GPL license) for download (for Mac OS X, Unix and Microsoft Windows) from the SourceForge web site: http://easyfig. Read More
BMC Bioinformatics 2006 Apr 27;7:225. Epub 2006 Apr 27.
Department of Plant and Microbial Biology, 461 Koshland Hall, University of California Berkeley, CA 94720-3102, USA.
Background: Two-dimensional data colourings are an effective medium by which to represent three-dimensional data in two dimensions. Such "color-grid" representations have found increasing use in the biological sciences (e.g. Read More
BMC Genomics 2016 Jan 13;17:49. Epub 2016 Jan 13.
Department of Psychiatry, University of Miami Miller School of Medicine, Miami, FL, 33136, USA.
Background: Next generation sequencing (NGS) technologies are indispensable for molecular biology research, but data analysis represents the bottleneck in their application. Users need to be familiar with computer terminal commands, the Linux environment, and various software tools and scripts. Analysis workflows have to be optimized and experimentally validated to extract biologically meaningful data. Read More