Glimma: interactive graphics for gene expression analysis

Bioinformatics
Shian SuMatthew E Ritchie

Abstract

graphics for RNA-sequencing and microarray gene expression analyses may contain upwards of tens of thousands of points. Details about certain genes or samples of interest are easily obscured in such dense summary displays. Incorporating interactivity into summary plots would enable additional information to be displayed on demand and facilitate intuitive data exploration. The open-source Glimma package creates interactive graphics for exploring gene expression analysis with a few simple R commands. It extends popular plots found in the limma package, such as multi-dimensional scaling plots and mean-difference plots, to allow individual data points to be queried and additional annotation information to be displayed upon hovering or selecting particular points. It also offers links between plots so that more information can be revealed on demand. Glimma is widely applicable, supporting data analyses from a number of well-established Bioconductor workflows ( limma , edgeR and DESeq2 ) and uses D3/JavaScript to produce HTML pages with interactive displays that enable more effective data exploration by end-users. Results from Glimma can be easily shared between bioinformaticians and biologists, enhancing reporting capabilities while...Continue Reading

References

Dec 18, 2014·Genome Biology·Michael I LoveSimon Anders
Jan 22, 2015·Nucleic Acids Research·Matthew E RitchieGordon K Smyth

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Citations

Jan 16, 2018·F1000Research·Monther AlhamdooshMatthew E Ritchie
Jul 6, 2018·American Journal of Physiology. Lung Cellular and Molecular Physiology·Lorise C GahringScott W Rogers
Nov 9, 2018·Nucleic Acids Research·Jarny ChoiChristine A Wells
Nov 19, 2019·Database : the Journal of Biological Databases and Curation·Alessandro La FerlitaAlfredo Pulvirenti
Jun 16, 2019·The Journal of Experimental Medicine·Maho NagasawaSuzanne M Bal
Jun 17, 2016·F1000Research·Charity W LawMatthew E Ritchie
May 2, 2018·Therapeutic Innovation & Regulatory Science·Jeremy WildfireJack G Modell
Oct 12, 2019·Science·Mauricio A ReynosoJulia Bailey-Serres
Feb 23, 2019·Nucleic Acids Research·Scott GiganteMatthew E Ritchie
Sep 14, 2020·The Plant Journal : for Cell and Molecular Biology·Susan M MoengaDouglas R Cook
Dec 11, 2020·BMC Bioinformatics·Federico MariniHarald Binder
Dec 17, 2020·BMJ Open Gastroenterology·Hanna Gustafsson BragdeJan Söderman
Jan 14, 2021·Scientific Reports·Naiara G BediagaLeonard C Harrison
Jul 6, 2020·Domestic Animal Endocrinology·L V MadozR L de la Sota
Mar 4, 2021·Current Biology : CB·Aishwarya KorgaonkarDavid L Stern
Nov 14, 2020·ELife·Iromi WanigasuriyaMarnie E Blewitt
Dec 11, 2020·European Journal of Immunology·Lisette KrabbendamJochem H Bernink
May 23, 2021·Scientific Reports·Iram Pablo Rodríguez-SanchezGustavo Ponce-Garcia
Jul 21, 2021·Nature Immunology·Hyungseok SeoPatrick G Hogan

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