ordinalbayes

Installing ordinalbayes

1. Install JAGS https://mcmc-jags.sourceforge.io
2. Install R https://cran.r-project.org
3. Install runjags which is hosted on CRAN and http://runjags.sourceforge.net
4. Install Bioconductor packages
   1. See https://www.bioconductor.org/install/ to install base Bioconductor packages
   2. To run examples using finalSet and reducedSet the DESeq2 package is needed. To install run
   > BiocManager::install("DESeq2")
5. Install ordinalbayes using
   1. Within R use > install.packages("ordinalbayes")
   or
   2. > devtools::install_github("kelliejarcher/ordinalbayes", build_vignettes = TRUE)
   This latter command takes longer because the vignette needs to be built.

References

1. Archer KJ, Seffernick AE, Sun, S, Zhang, Y. ordinalbayes: Fitting ordinal Bayesian regression models to high-dimensional data using R. STATS, 5(2), 371-384, 2022. https://doi.org/10.3390/stats5020021
2. Zhang Y, Archer KJ. Bayesian variable selection for high-dimensional data with an ordinal response: identifying genes associated with prognostic risk group in acute myeloid leukemia. BMC Bioinformatics, 22:539, 2021. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8565083/
3. Zhang Y, Archer KJ. Bayesian penalized cumulative logit model for high-dimensional data with an ordinal response. Statistics in Medicine, 40:1453-1481, 2021. https://pubmed.ncbi.nlm.nih.gov/33336826/