Coleman Breen's repositories
UNC_Science_Expo_2018
Interactive Shiny Applicatino in R to demonstrate the hazards of spurious correlations. App can be found at https://cbreen.shinyapps.io/final_app/
850k-BMI
Scripts used to analyze EPIC 850k arrays for associations with BMI
cbreenmachine.github.io
Github Pages template for academic personal websites, forked from mmistakes/minimal-mistakes
deep-learning-sandbox
Notebooks to demonstrate basic deep learning concepts.
eda-meQTL
Quick exploratory analysis of meQTL in LOAD project
genplot
Miscellaneous genomics plots
GWAS-project
Code for final project for BMI 826.
meAD-fq2bed
Pipeline used to take raw fastq files, trim, map, and process to methylated / coverage bed files
meAD-models-targets
Targeted version of meAD-models pipeline
meAD-paper
Analysis of methylation data from Late-onset AD cohort
methy-seq-gemBS-processing
Rewrite of methylation processing pipeline using snakemake
Rray
Idioms and workflows used frequently in EPIC 850K array analysis
safe-haven
Some notebooks to convince myself of concepts from Spitznagel's "Safe Haven"
seq-to-methy-preprocesing
Running the scripts to encode variants, filter by coverage, and standardize covariates.
snv-methy-preprocessing
EDA and prototyping
vencoder
Python module to encode variants in a variety of schemes.
volplot
Volcano plot
wiscR
R package with my favorite functions, idioms, etc. during grad school at Wisconsin