To install this package, start R and enter:

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

In most cases, you don't need to download the package archive at all.

MEDIPS

(MeD)IP-seq data analysis

Bioconductor version: Release (2.14)

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>

To install this package, start R and enter:

Citation (from within R, enter citation("MEDIPS")):

Installation

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, Preprocessing, QualityControl, Sequencing, Software, Visualization
Version 1.14.0
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_1.14.0.tar.gz
Windows Binary MEDIPS_1.14.0.zip (32- & 64-bit)
Mac OS X 10.6 (Snow Leopard) MEDIPS_1.14.0.tgz
Mac OS X 10.9 (Mavericks) MEDIPS_1.14.0.tgz
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