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Related Experiment Video

Updated: Mar 17, 2026

Targeted RNA Sequencing Assay to Characterize Gene Expression and Genomic Alterations
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regionReport: Interactive reports for region-level and feature-level genomic analyses.

Leonardo Collado-Torres1, Andrew E Jaffe2, Jeffrey T Leek3

  • 1Department of Biostatistics, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland, 21205, USA; Lieber Institute for Brain Development, Johns Hopkins Medical Campus, Baltimore, Maryland, 21205, USA; Center for Computational Biology, Johns Hopkins University, Baltimore, Maryland, 21205, USA.

F1000Research
|July 29, 2016
PubMed
Summary

The regionReport R package generates interactive genomic analysis reports for RNA-seq data. It aids in exploring differential expression results and ensures reproducible research.

Keywords:
ChIP-seqGenomicsInteractiveRNA-seqReportReproducibilitySequencingSoftware

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Area of Science:

  • Genomics
  • Bioinformatics
  • Computational Biology

Background:

  • Genomic and RNA-sequencing (RNA-seq) analyses generate large datasets requiring robust interpretation tools.
  • Interactive and reproducible reporting is crucial for disseminating complex biological findings.

Purpose of the Study:

  • To introduce regionReport, an R package designed for generating detailed interactive reports from genomic and RNA-seq data.
  • To provide specialized reports for common differential expression analysis pipelines.

Main Methods:

  • The regionReport package utilizes R to process and visualize genomic region and feature-level data.
  • It integrates quality control, results overview, interactive tables, and reproducibility information.
  • The package supports differential expression analysis results from DESeq2, edgeR, and derfinder.

Main Results:

  • regionReport generates comprehensive, interactive reports that enhance the exploration of genomic and RNA-seq results.
  • The package offers specialized reporting modules for popular differential expression analysis tools.
  • Its flexible design allows for the addition of new report templates for other analysis pipelines.

Conclusions:

  • regionReport provides a valuable tool for researchers to create detailed, interactive, and reproducible reports from genomic and RNA-seq analyses.
  • The package facilitates the interpretation and communication of differential expression findings.
  • Its extensibility ensures its continued relevance for various bioinformatics workflows.