The goal of compareRhythms is to find features with altered circadian rhythm parameters (amplitude and phase) between the control and experimental groups.
You can install the current version of compareRhythms from GitHub with:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install(version = "3.15") # This installs bioconductor
BiocManager::install(c("SummarizedExperiment", "DESeq2", "edgeR", "limma", "rain")) # Packages needed by compareRhythms
install.packages("devtools") # if it is not already installed
devtools::install_github("cran/npsm") # Package archived by CRAN
devtools::install_github("cran/DODR") # Package archived by CRAN
devtools::install_github("bharathananth/compareRhythms", build_vignettes = TRUE, dependencies = TRUE)The analysis is run using a single function compareRhythms(). To
execute this function, the three necessary ingredients are the
timeseries data, the experimental design and parameters to choose and
tune the method. The output of the function is a data.frame with the
IDs of the differentially rhythmic features, the category it is
classified under and optionally the rhythm parameters of the feature in
the two groups. The differential rhythmicity categories are gain of,
loss of, change of, or same rhythms (with respect to the
reference/control group).
For complete examples, please refer to the vignette titled User Guide by running
library(compareRhythms)
vignette("UserGuide", package="compareRhythms")Please cite compareRhythms in publications as:
- Software v1.0.0 https://doi.org/10.5281/zenodo.7699722
- Venn diagram analysis overestimates the extent of circadian rhythm reprogramming. FEBS J, 289: 6605-6621. https://doi.org/10.1111/febs.16095
The R code to perform all the analyses in this publication (using compareRhythms) can be found in the repository https://github.com/bharathananth/FEBSJ-VDA-overestimates
If you encounter a bug, please file a minimal reproducible example on github.