Technical

You can find technical posts here that will help you with something you are trying to do.

A guide to designs and contrasts in DESeq2

Many statistical analysis packages in R utilize design matrices for setting up comparisons between data subsets. The two Bioconductor packages most commonly used for…

Cox proportional hazards with correlated variables

Cox proportional hazards (CoxPH) model is a common approach to study the occurrence of an event as a factor of time. In medical studies, CoxPH is used to model patient…

Programmatically create new headings and outputs in Rmarkdown

I often find myself performing analyses looped over certain parts of the data in my Rmarkdown. I like seeing the output under different headings in the final output for easy…

Understanding Lasso and Ridge Regression

We have been using machine learning algorithms (specifically lasso and ridge regression) to identify the genes that correlate with different clinical outcomes in cancer.…

Useful YAML options for generating HTML reports in R

I think most people start using R with scripts initially. Scripts are great for modular computational tasks, but for generating informative reports, Rmarkdown is a must. Rmd…

Annotating unknown clusters in scRNAseq data using CIPR:A cross-species reference comparison

We have recently published a Shiny (R) app called Cluster Identity Predictor (CIPR) in BMC Bioinformatics that helps annotate unknown clusters in single cell RNAseq…