MicroScope: RNA-seq software analysis suite for gene expression heatmaps

Posted by: RNA-Seq Blog in Data Visualization June 3, 2016 3,745 Views

Researchers at the University of Miami Miller School of Medicine have developed a user-friendly ChIP-seq and RNA-seq software suite for the interactive visualization and analysis of gene expression heatmaps, including integrated features to support: principal component analysis, differential expression analysis, gene ontology analysis, and dynamic network visualization of genes directly from a heatmap.

MicroScope user interface

MicroScope UI showcasing the magnification feature as well as features such as: sample file download, sample input, buffer size, log2 data transformation, multiple heatmap color schemes, hierarchical clustering, row/column dendrogram branch coloring, row/column font size, and heatmap download button. Additional UI features are sequentially unlocked as the user progresses through the MicroScope software suite.

Availability – MicroScope is hosted online as an R Shiny web application based on the D3 JavaScript library: http://microscopebioinformatics.org/ The methods are implemented in R, and are available as part of the MicroScope project at: https://github.com/Bohdan-Khomtchouk/Microscope.

Khomtchouk BB, Hennessy J, Dargis-Robinson V, Wahlestedt C. (2016) MicroScope: ChIP-seq and RNA-seq software analysis suite for gene expression heatmaps. bioRXiv [Epub ahead of print]. [abstract]