README.md

In GabrielHoffman/decorate: Differential Epigenetic Coregulation Test

Differential Epigenetic Correlation Test

Install

library(devtools)

# Install decorate
#   first, check for Bioconductor
if (!requireNamespace("BiocManager", quietly = TRUE)){
    cat("Please install Bioconductor before continuing:\n")
    cat("see http://bioconductor.org/install/\n\n")
}else{
    install_github('GabrielHoffman/decorate', repos=BiocManager::repositories())
}   

Dependencies

Depending on your system, you may need to install these system dependencies first:

• udunits
• proj
• gdal
• geos

Mac OS X

brew install udunits proj gdal geos

Ubuntu

apt-get install libudunits2-dev libproj-dev proj-data proj-bin libgeos-dev libgeos-c1v5 libgdal-dev

CentOS

yum install udunits2-devel
yum install proj-devel
yum install gdal-devel
yum install geos-devel

Windows

decorate should install on Windows without needing to install these dependencies.

Data analysis from manuscript

• DNA methylation from kidney renal clear cell carcinoma
• DNA methylation from schizophrenia brains
• ATAC-seq from schizophrenia brains
• Histone modification ChIP-seq from human brain

Simulations and properties of methods

• Simulations

Results files

Analysis code

GabrielHoffman/decorate documentation built on May 23, 2023, 1:29 a.m.