A set of scripts and functions for analyzing MeDIP-seq datasets
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data
functions
README.md
annotateDMRs.R
blastAnnotate.R
customFunctions.R
dataNames.R
generateReports.R
getReadDepth.R
identifyApoDmr.R
medipAnalysis.R
medipAnalysisAdd.R
medipAnalysisLM.R
medipAnalysisNorm.R
medipProcessing.R
medipReport.Rmd
medipReport_APO.Rmd
medipSummary.Rmd
pairwiseReport.Rmd
prepareData.R
publicationFiles.R

README.md

medipPipeline

A collection of scripts for MeDIP-seq data analysis

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.

Availability

medipPipeline is available at https://github.com/skinnerlab/MeDIP-seq

Overview

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.

medipAnalysisLM.R: This is a low memory version of medipAnalysis.R.

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.

publicationFiles.R: Produces separate files for selected tables and plots.