christensen-lab-dartmouth Goto Github PK

analysis-example-codes

R scripts from Ze Zhang often used in DNA methylation analyses. Not the most clean but should be helpful

brca_lowstage_dmgrs

The repository stores the analytical code for the pre-release of the manuscript titled "Tumor subtype and cell type independent DNA methylation alternations reveals twelve genes associated with low stage breast carcinoma".

cf_epigenetics

R code repository for statistical analysis and data visualization of manuscript "Genome-wide DNA methylation profiling shows a distinct epigenetic signature associated with Lung Macrophages in cystic fibrosis"

hnscc-mirsnp-survival

lab-tutorials

Programming tutorials for the Christensen Lab

methyl_capsule_data

Stores data for capsule-related projects

methylcapsnet

methyliftover

A utility to map bisulfite sequencing data to the Illumina 450K methylation CpG set

methylnet

Modular framework for deep learning predictions on methylation data.

normal-breast-5hmc

normal-breast-methylation

oxybs

Vignette for data processing and use of the fitOxBS function from the OxyBS R package

pcns_5hmc_06112020

Measurement of 5hmC in pediatric cns tumors

pymethylprocess

Preprocessing methylation pipeline, written in python. Easy to use and highly parallelized.

shared_450k_annotation

vae_analysis

DNA methylation analysis using VAE

vae_methylation

VAE methylation analysis using the Tybalt model developed by Way et al.