bactcountr is an R package that provides an automated way to calculate Colony Forming Units (CFUs) based on the dilutions used. It then calculates statistical significance and plots the final results. All of the code for this package can be found on my github page: https://github.com/aef1004/bactcountr.
NanoString nCounter is a technology used to assess gene expression data. I was recently approached by a colleague that spent weeks copy and pasting data into GraphPad to analyze the the data. In response, I built a pipeline that performs automated statistical analysis for the Nanostring data. The pipeline reads in and cleans the data that contains hundreds of genes per study animal. It then tests each gene-mouse group pair for normality, similar variances, and then performs the appropriate statistical test (t-test or Wilcox Mann-Whitney) based on the results.
Flow cytometers can now analyze up to 50 parameters per cell and millions of cells per sample; however, conventional methods to analyze data are subjective and time-consuming. To address these issues, we have developed a novel analysis pipeline to identify a plethora of cell populations efficiently. Coupled with feature engineering and immunological context, researchers can immediately extrapolate novel discoveries through easy-to-understand plots. The R-based pipeline uses Fluorescence Minus One (FMO) controls or distinct population differences to develop thresholds for positive/negative marker expression.
Using the Academia Hugo theme developed by Michael Vahn, I have developed this website using R blogdown, Github, and the web-service Netlify. All of the code for this website can be found on my github page: https://github.com/aef1004/blogdown_academia_2020.