Journal article

Glimma: interactive graphics for gene expression analysis

Shian Su, Charity W Law, Casey Ah-Cann, Marie-Liesse Asselin-Labat, Marnie E Blewitt, Matthew E Ritchie

BIOINFORMATICS | OXFORD UNIV PRESS | Published : 2017

Abstract

Motivation: 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. Results: 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 addit..

View full abstract

Grants

Awarded by National Health and Medical Research Council (NHMRC)


Funding Acknowledgements

This work was supported by the National Health and Medical Research Council (NHMRC) (Project grants 1050661 (MER, MLAL), 1045936 (MEB, MER), 1079756 (MLAL, MEB, MER) and 1059622 (MEB, MER); Fellowships 1104924 (MER) and 1110206 (MEB)), a Viertel Fellowship (MLAL), Victorian State Government Operational Infrastructure Support and Australian Government NHMRC IRIISS.