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regionReport: Interactive reports for region-level and feature-level genomic analyses [version 2; referees: 2 approved, 1 approved with reservations]

Authors :
Leonardo Collado-Torres
Andrew E. Jaffe
Jeffrey T. Leek
Author Affiliations :
<relatesTo>1</relatesTo>Department of Biostatistics, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland, 21205, USA<br /><relatesTo>2</relatesTo>Lieber Institute for Brain Development, Johns Hopkins Medical Campus, Baltimore, Maryland, 21205, USA<br /><relatesTo>3</relatesTo>Center for Computational Biology, Johns Hopkins University, Baltimore, Maryland, 21205, USA<br /><relatesTo>4</relatesTo>Department of Mental Health, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland, 21205, USA
Source :
F1000Research. 4:105
Publication Year :
2016
Publisher :
London, UK: F1000 Research Limited, 2016.

Abstract

regionReport is an R package for generating detailed interactive reports from region-level genomic analyses as well as feature-level RNA-seq. The report includes quality-control checks, an overview of the results, an interactive table of the genomic regions or features of interest and reproducibility information. regionReport provides specialised reports for exploring DESeq2, edgeR, or derfinder differential expression analyses results. regionReport is also flexible and can easily be expanded with report templates for other analysis pipelines.

Subjects

Subjects :
Software Tool Article
Articles
Bioinformatics
Genomics
Medical Genetics
Report
Interactive
Reproducibility
Sequencing
ChIP-seq
RNA-seq
Software

Details

ISSN :
20461402
Volume :
4
Database :
F1000Research
Journal :
F1000Research
Notes :
Revised Amendments from Version 1 We would like to thank the reviewers for their excellent reviews and valuable feedback. We have taken into consideration all of the reviews and comments, and have improved the software, updated the software vignettes, and added more figures to the manuscript. In particular we merged David Robinson's pull request, added the customCode argument, provide code for making histograms instead of density plots which is used in one of the example use cases, and requested that quotation marks are typeset in a way that makes them easy to copy-paste into R; made it easier to use and install dependencies via a new function load_install() based on Karthik Ram's feedback, added a link to the bibliography file; modified the manuscript and added more example use cases to motivate users to use regionReport, particularly with DESeq2 or edgeR results which expands the software's usefulness to a broader user base. This manuscript matches the software release from Bioconductor version 3.3 which uses by default rmarkdown's version 0.9.5 capabilities. We considered using git2r and have not added support for so far given that (A) we mostly use regionReport in git-controlled directories that are not on the gh-pages branch and (B) that some of the reports can be large in size. However, we might add a function for uploading the resulting report to GitHub via git2r in the future., , [version 2; referees: 2 approved, 1 approved with reservations]
Publication Type :
Academic Journal
Accession number :
edsfor.10.12688.f1000research.6379.2
Document Type :
software-tool
Full Text :
https://doi.org/10.12688/f1000research.6379.2
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