Pinned Repositories
240312-seq-stats
Compute summary statistics for aligned sequencing files.
850k-BMI
Scripts used to analyze EPIC 850k arrays for associations with BMI
axonregen
badger
cbreenmachine.github.io
Github Pages template for academic personal websites, forked from mmistakes/minimal-mistakes
data-science-problems
Foundational data science techniques--scraping, cleaning, exploratory analysis--on wide range of topics.
deep-learning-sandbox
Notebooks to demonstrate basic deep learning concepts.
methy-load
ring-labeler
Neural network architecture to classify pixels in image as signal/noise.
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/
cbreenmachine's Repositories
cbreenmachine/methy-load
cbreenmachine/240312-seq-stats
Compute summary statistics for aligned sequencing files.
cbreenmachine/850k-BMI
Scripts used to analyze EPIC 850k arrays for associations with BMI
cbreenmachine/axonregen
cbreenmachine/badger
cbreenmachine/cbreenmachine.github.io
Github Pages template for academic personal websites, forked from mmistakes/minimal-mistakes
cbreenmachine/deep-learning-sandbox
Notebooks to demonstrate basic deep learning concepts.
cbreenmachine/eda-meQTL
Quick exploratory analysis of meQTL in LOAD project
cbreenmachine/genplot
Miscellaneous genomics plots
cbreenmachine/goplot
cbreenmachine/HPC-notes
Notes from Dan Negrut's High-Performance Computing Class (ME 759)
cbreenmachine/LOAD-850k-analysis
cbreenmachine/LOAD-DMPs-browser
cbreenmachine/me-hc-bayes
cbreenmachine/meAD-850k
cbreenmachine/meAD-fq2bed
Pipeline used to take raw fastq files, trim, map, and process to methylated / coverage bed files
cbreenmachine/meAD-models
cbreenmachine/meAD-models-targets
Targeted version of meAD-models pipeline
cbreenmachine/meAD-paper
Analysis of methylation data from Late-onset AD cohort
cbreenmachine/meAD-UCSC-tracks
cbreenmachine/methy-process-v2
A re-write of the whole-genome methylation sequencing processing pipeline.
cbreenmachine/methy-seq-gemBS-processing
Rewrite of methylation processing pipeline using snakemake
cbreenmachine/RNAseqElegans
cbreenmachine/Rray
Idioms and workflows used frequently in EPIC 850K array analysis
cbreenmachine/safe-haven
Some notebooks to convince myself of concepts from Spitznagel's "Safe Haven"
cbreenmachine/seq-to-methy-preprocesing
Running the scripts to encode variants, filter by coverage, and standardize covariates.
cbreenmachine/seq-to-methy-public-data
Processing meQTL, interactions, etc.
cbreenmachine/snv-methy-preprocessing
EDA and prototyping
cbreenmachine/vencoder
Python module to encode variants in a variety of schemes.
cbreenmachine/volplot
Volcano plot