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RNA sequencing, or RNA-Seq, is a high-throughput sequencing technology used to study the transcriptome of a cell. Transcriptomics helps to interpret the functional elements of a genome and identify the molecular constituents of an organism. Additionally, it also helps in understanding the development of an organism and the occurrence of diseases.
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Updated: Mar 14, 2026

Targeted RNA Sequencing Assay to Characterize Gene Expression and Genomic Alterations

Targeted RNA Sequencing Assay to Characterize Gene Expression and Genomic Alterations

Published on: August 4, 2016

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

Bohdan B Khomtchouk¹, James R Hennessy², Claes Wahlestedt³

¹Center 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. b.khomtchouk@med.miami.edu.

BMC Bioinformatics

|September 24, 2016

Summary

This summary is machine-generated.

This study introduces MicroScope, a user-friendly software suite for interactive genomic data visualization and analysis. It integrates multiple analysis types for ChIP-seq and RNA-seq data, enhancing multi-scale genomic insights.

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Area of Science:

Genomics
Bioinformatics
Data Visualization

Background:

Heatmaps are essential for analyzing next-generation sequencing (NGS) data.
Traditional heatmap tools lack multi-scale analysis and integration across diverse genomic datasets (ChIP-seq, RNA-seq).
Genomic analysis requires integrated tools for various data types and analysis layers.

Purpose of the Study:

To develop a user-friendly software suite for interactive genomic data visualization and analysis.
To integrate multiple analysis types within a single platform for ChIP-seq and RNA-seq data.
To provide multi-scale insight across different genomic analysis layers.

Main Methods:

Development of an R Shiny web application utilizing the D3 JavaScript library.
Implementation of integrated features for differential expression analysis, interactive heatmap production, principal component analysis, gene ontology analysis, and network analysis.
Creation of a software suite for ChIP-seq and RNA-seq data analysis.

Main Results:

A user-friendly software suite named MicroScope has been developed.
The suite offers interactive visualization and analysis of genomic data.
Integrated features support a wide range of genomic analyses for ChIP-seq and RNA-seq.

Conclusions:

MicroScope is available as an online R Shiny web application.
The software is accessible via a GitHub repository.
The developed methods enhance the analysis of diverse genomic datasets.