source("http://bioconductor.org/biocLite.R")
biocLite("MEDIPS")

MEDIPS

(MeD)IP-seq data analysis

Bioconductor version: 2.13

MEDIPS was developed for analyzing data derived from methylated DNA immunoprecipitation (MeDIP) experiments followed by sequencing (MeDIP-seq). However, MEDIPS provides several functionalities for the analysis of other kinds of quantitative sequencing data (e.g. ChIP-seq, MBD-seq, CMS-seq and others) including calculation of differential coverage between groups of samples as well as saturation and correlation analyses.

Author: Lukas Chavez, Matthias Lienhard, Joern Dietrich

Maintainer: Lukas Chavez <lchavez at liai.org>

Installation

To install this package, start R and enter:

source("http://bioconductor.org/biocLite.R")
biocLite("MEDIPS")

Documentation

To view documentation for the version of this package installed in your system, start R and enter:

browseVignettes("MEDIPS")

 

PDF	R Script	MEDIPS
PDF		Reference Manual

Details

biocViews	ChIPseq, CpGIsland, DNAMethylation, DifferentialExpression, HighThroughputSequencing, Preprocessing, QualityControl, Sequencing, Software, Visualization
Version	1.12.0
In Bioconductor since	BioC 2.7 (R-2.12)
License	GPL (>=2)
Depends	R (>= 3.0), BSgenome, DNAcopy
Imports	Biostrings, BSgenome, Rsamtools, graphics, gtools, IRanges, methods, stats, utils, GenomicRanges, edgeR, GenomicFeatures, DNAcopy, biomaRt, rtracklayer
Suggests	BSgenome, BSgenome.Hsapiens.UCSC.hg19, MEDIPSData
System Requirements
URL
Depends On Me
Imports Me
Suggests Me

Package Archives

Follow Installation instructions to use this package in your R session.

Package Source	MEDIPS_1.12.0.tar.gz
Windows Binary	MEDIPS_1.12.0.zip (32- & 64-bit)
Mac OS X 10.6 (Snow Leopard)	MEDIPS_1.12.0.tgz
Browse/checkout source	(username/password: readonly)
Package Downloads Report	Download Stats