This repository currently contains a collection of R scripts and functions for analyzing MeDIP-seq datasets. Eventually these scripts will form a pipeline that can be used on generic datasets.
medipPipeline is available at https://github.com/skinnerlab/MeDIP-seq
dataNames.R: Configuration file for the pipeline. It contains filenames, file locations, constants, and other adjustable parameters.
prepareData.R: Cleans, filters (Trimmomatic), and maps (Bowtie2) reads as well as generates read quality reports (FastQC).
medipAnalysis.R: Performs the basic MeDIP-seq analysis using the MEDIPS R library.
medipProcessing.R: Identifies DMR and generates DMR tables.
annotateDMRs.R: Adds annotation information to DMR tables.
customFunctions.R: Wrapper for loading all custom functions used by the pipeline. These functions are stored in the functions folder.
generateReports.R: Wrapper for generating reports summarizing the MeDIP-seq results. This script renders the report using the mediepReport.Rmd code.