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

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Abstract

Background: Heatmaps are an indispensible visualization tool for examining large-scale snapshots of genomic activity across various types of next-generation sequencing datasets. However, traditional heatmap software do not typically offer multi-scale insight across multiple layers of genomic analysis (e.g., differential expression analysis, principal component analysis, gene ontology analysis, and network analysis) or multiple types of next-generation sequencing datasets (e.g., ChIP-seq and RNA-seq). As such, it is natural to want to interact with a heatmap's contents using an extensive set of integrated analysis tools applicable to a broad array of genomic data types. Results: We propose a user-friendly ChIP-seq and RNA-seq software suite for the interactive visualization and analysis of genomic data, including integrated features to support differential expression analysis, interactive heatmap production, principal component analysis, gene ontology analysis, and dynamic network analysis. Conclusions: 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.

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Khomtchouk, B. B., Hennessy, J. R., & Wahlestedt, C. (2016). MicroScope: ChIP-seq and RNA-seq software analysis suite for gene expression heatmaps. BMC Bioinformatics, 17(1). https://doi.org/10.1186/s12859-016-1260-x

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