Our Code Repositories

Here at the complex disease epigenetics group, we believe that our code should be easily accessible to aid in reproducing the results in our research.
As such, we share our published code via GitHub. This page contains our featured repositories.

Our Shiny Apps

We believe that reproducibility and accessibility are crucial for scientific progress.
To that end, we develop and share interactive R Shiny apps to make our analyses and visualizations readily available to the research community.

EPICDNAmPowerCalcs

Web app designed to perform power calculations for DNA methylation studies.

LRBrainCoverage

Summary of isoform expression values in human cortex from long-read transcriptome sequencing

MetaAna

Meta-analysis of epigenome-wide association studies in Alzheimer's disease

SMR

Leveraging DNA methylation quantitative trait loci to characterize the relationship between methylomic variation, gene expression and complex traits.

Publication data

We strongly believe in the importance of open and accessible data for scientific reproducibility.
To support this, we make the data from our publications readily available for download. This page provides links to our published datasets.

Allelic Expression data

Stochastic choice of allelic expression in human neural stem cells

Allelic skewing data

Allelic skewing of DNA methylation is widespread across the genome

Blood Brain DNA Methylation Comparison Tool

HABIT

Hydroxymethylation Annotation in Brain Integrative Tool (HABIT)

Alzheimer's disease H3K27ac data

A histone acetylome-wide association study of Alzheimer's disease

MeDIP-Seq brain data

Tissue-specific epigenetic variation across brain and blood: functional annotation of the human brain methylome

Human fetal brain Methylomic trajectories

Methylomic trajectories across human fetal brain development

Monozygotic twin data

Disease-associated epigenetic changes in monozygotic twins discordant for schizophrenia and bipolar disorder

Tissue-specific patterns of allelically-skewed DNA methylation

XXY karyotype data

Epigenomic and transcriptomic signatures of a 47,XXY karyotype in the brain

Human cortex isoform data

Long-read sequencing reveals novel transcripts in human cortex, with age-related differences

Schizophrenia mQTL data

Methylation quantitative trait loci (mQTL) in the developing human brain and their enrichment in genomic regions associated with schizophrenia.