Tools & Data

CpG_Me: 

A whole-genome bisulfite sequencing (WGBS) pipeline for the analysis and QC of DNA methylation that goes from from raw reads to a CpG count matrix.

CpG_Me Flowchart
An overview of the CpG_Me workflow

DMRichR:

An executable and package for the statistical analysis and visualization of differentially methylated regions (DMRs) from CpG count matrices (Bismark cytosine reports).

DMRichR Workflow
An overview of the DMRichR workflow
Example DMR: Each dot represents the methylation level of an individual CpG in a single sample, where the size of the dot is representative of coverage. The lines represent smoothed methylation levels for each sample, either control (blue) or DS (red). Genic and CpG annotations are shown below the plot.
Example DMR: Each dot represents the methylation level of an individual CpG in a single sample, where the size of the dot is representative of coverage. The lines represent smoothed methylation levels for each sample, either control (blue) or DS (red). Genic and CpG annotations are shown below the plot.

comethyl:

An R package for weighted region comethylation network analysis (Under development).

comethyl workflow

cnv-caller:

A copy number variation (CNV) caller that detects large-scale variation in low coverage aligned whole genome bisulfite sequencing (WGBS) data (Under development).

cnv-caller workflow

GEO Data:

Cord blood DNA methylome in newborns later diagnosed with autism spectrum disorder reflects early dysregulation of neurodevelopmental and X-linked genes

A meta-analysis of two high-risk prospective studies reveals autism-specific transcriptional changes to chromatin, autoimmune, and environmental response genes in umbilical cord blood

Epigenomic signatures in liver and blood of Wilson disease patients include hypermethylation of liver-specific enhancers

Epigenetic changes of the thioredoxin system in the tx-j mouse model and in patients with Wilson disease

Snord116-dependent diurnal rhythm of DNA methylation in mouse cortex

Integrative epigenomic analyses of early-life hypothalamic response to augmented maternal care

Cumulative Impact of Polychlorinated Biphenyl and Large Chromosomal Duplications on DNA Methylation, Chromatin, and Expression of Autism Candidate Genes

The Human Placenta Methylome

Role of DNMT3B in the Regulation of Early Neural and Neural Crest Specifiers

Large-Scale Methylation Domains Mark a Functional Subset of Neuronally Expressed Genes

Integrated Epigenomic Analyses of Neuronal MeCP2 Reveal a Role for Long-Range Interaction With Active Genes

Identifying Targets of MeCP2 During Neuronal Maturational Differentiation