R User Group
The Ragland lab periodically organizes meetings to introduce and workshop useful packages and functions in R. When we are actively running a group, please contact Greg Ragland for access to the google group.
Materials from past meetings including powerpoints/pdfs and scripts are posted here.
Below are links to scripts that I have created over the course of my research career. Above each link is a brief description of what the script(s) does and what tasks it will help perform. I hope that this can help you in some way.
– Microarray correlations: This script takes microarray data from a collection of fly lines and correlates it to survival data that I obtained through cold shock assays
– The first script creates a GWAS file so that a Manhattan plot can be produced. Essentially the first script helps associate a likely-hood score to each loci so that the second script can produce a Manhattan plot with the R package, qqman
– These scripts perform basic statistics on a data set and produces simple scatter plots
– These scripts are similar to the ones above but do so at a more advanced level with many more options included, comparing things like rearing conditions, life stage, and stress type
– This script is a good one for creating boxplots
– This script will produce histograms
– This script will produce survival curves from survival data
– This script creates Venn diagrams from your data
– This script creates reaction norms for visualizing genotype x environment interactions. The second script attempts to create 3D reaction norms if there are three factors you are investigating
– This script takes data from different treatments, compares them, and calculates the effect size difference and supporting statistics
– This script calculates both heritabilities of traits and genetic correlations between two traits using bootstrapping and permutation
– These two scripts creates models for and analyzes differential expression from RNAseq datasets using the package EdgeR