Interfacing Bioconductor with tidyverse with tidySingleCellExperiment and tidySummarisedExperiment
Stefano Mangiola,Maria Doyle WEHI
Abstract
Recently, plyranges and tidybulk represented efforts toward the harmonization of transcriptomic data structures and workflows using the concept of data tidiness, to facilitate modularisation. In this workshop, we present tidySingleCellExperiment and tidySummarizedExperiment, two R packages that allow the user to visualise and manipulate SingleCellExperiment and SummarizedExperiment objects in a tidy fashion. Importantly, the framework tidybulk now works natively with SummarizedExperiment objects and, thanks to tidySummarizedExperiment, allow tidy and modular RNA sequencing analyses without renouncing to the efficiency of Bioconductor data containers. These tools are part of the tidytranscriptomic R software suite, and represent an effort toward the harmonisation of transcriptional analyses under the tidy umbrella.
Keywords: Transcriptomics,tidyverse,SingleCellExperiment,SummarizedExperiment,tidy