A collection of functions for the analysis and visualization of the MoTrPAC PASS1B white adipose tissue (WAT) data as provided in the MotrpacRatTraining6moData package. This package was built specifically to generate the MotrpacRatTraining6moWATData package, so much of it is tailored only for use with those datasets, though users may find some of the functionality contained herein to be useful in other projects:
- Differential analysis (DA) with the limma and edgeR packages
- Fast Gene Set Enrichment Analysis (FGSEA) with fgsea and msigdbr
- Kinase-Substrate Enrichment Analysis (KSEA) with PhosphoSitePlus
- Over-representation analysis (ORA)
- Weighted Gene Co-expression Network Analysis (WGCNA)
Installation
Install this package with devtools:
if (!require("devtools", quietly = TRUE))
install.packages("devtools")
devtools::install_github("MoTrPAC/MotrpacRatTraining6moWAT")Preprint
Many, G. M., Sanford, J. A., Sagendorf, T. J., Hou, Z., Nigro, P., Whytock, K., Amar, D., Caputo, T., Gay, N. R., Gaul, D. A., Hirshman, M., Jimenez-Morales, D., Lindholm, M. E., Muehlbauer, M. J., Vamvini, M., Bergman, B., Fernández, F. M., Goodyear, L. J., Ortlund, E. A., … Schenk, S. (2023). Sexual dimorphism and the multi-omic response to exercise training in rat subcutaneous white adipose tissue. BioRxiv. https://doi.org/10.1101/2023.02.03.527012