MicroScope

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

Bohdan B. Khomtchouk, James R. Hennessy, Claes R Wahlestedt

Research output: Contribution to journalArticle

5 Citations (Scopus)

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.

Original languageEnglish (US)
Article number390
JournalBMC Bioinformatics
Volume17
Issue number1
DOIs
StatePublished - Sep 22 2016

Fingerprint

Gene Ontology
Principal Component Analysis
RNA
Gene expression
Microscope
Gene Expression
Microscopes
Chip
Software
Electric network analysis
Principal component analysis
Ontology
Gene Regulatory Networks
Visualization
Genes
Genomics
Libraries
Differential Expression
Network Analysis
Sequencing

ASJC Scopus subject areas

  • Structural Biology
  • Biochemistry
  • Molecular Biology
  • Computer Science Applications
  • Applied Mathematics

Cite this

MicroScope : ChIP-seq and RNA-seq software analysis suite for gene expression heatmaps. / Khomtchouk, Bohdan B.; Hennessy, James R.; Wahlestedt, Claes R.

In: BMC Bioinformatics, Vol. 17, No. 1, 390, 22.09.2016.

Research output: Contribution to journalArticle

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