Robust longitudinal Differential Expression (RolDE), is a composite method, consisting of three independent modules with different approaches to detecting longitudinal differential expression. The RegROTS module combines individual regression modelling with the power of the established differential expression method Reproduciblity Optimized Test Statistic (ROTS). In the DiffROTS module, the expression between all the individuals in the different conditions is directly compared at all timepoints. The PolyReg module uses polynomial regression modelling to evaluate longitudinal differential expression. The combination of these modules allows RolDE to robustly detect differences in longitudinal trends and expression levels in diverse data types and experimental settings.
Contrary to many existing approaches, the RolDE does not require prior knowledge concerning the types of differences searched, but can easily be applied even by non-experienced users.
The latest version of RolDE can be downloaded from GitHub using the devtools R package:
devtools::install_github(repo = "https://github.com/elolab/RolDE", build_vignettes = T)
The build_vignettes parameter should be set to TRUE to enable the building of instructions and examples for RolDE usage.
The latest release of RolDE can also be installed from Bioconductor:
if (!requireNamespace("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("RolDE")
RolDE comes with a detailed documentation and a detailed set of instuctions. The documentation of RolDE can be simply accessed after installation and loading the package by:
?RolDE
For detailed instuctions and examples on how to use RolDE, please view the included vignettes:
browseVignettes("RolDE")
If you have comments regarding RolDE, please contact us here.