To install this package, start R and enter:

## try http:// if https:// URLs are not supported
source("https://bioconductor.org/biocLite.R")
biocLite("MEDIPS")

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

MEDIPS

This package is for version 3.2 of Bioconductor; for the stable, up-to-date release version, see MEDIPS.

DNA IP-seq data analysis

Bioconductor version: 3.2

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

Author: Lukas Chavez, Matthias Lienhard, Joern Dietrich, Isaac Lopez Moyado

Maintainer: Lukas Chavez <l.chavez at dkfz.de>

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

Installation

To install this package, start R and enter:

## try http:// if https:// URLs are not supported
source("https://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 MEDIPS
PDF Reference Manual

Details

biocViews ChIPSeq, CopyNumberVariation, Coverage, CpGIsland, DNAMethylation, DifferentialExpression, Genetics, GenomeAnnotation, Microarray, Preprocessing, QualityControl, SequenceMatching, Sequencing, Software, Visualization
Version 1.20.1
In Bioconductor since BioC 2.7 (R-2.12) (5.5 years)
License GPL (>=2)
Depends R (>= 3.0), BSgenome, Rsamtools
Imports GenomicRanges, Biostrings, graphics, gtools, IRanges, methods, stats, utils, edgeR, DNAcopy, biomaRt, rtracklayer, preprocessCore
LinkingTo
Suggests BSgenome.Hsapiens.UCSC.hg19, MEDIPSData, BiocStyle
SystemRequirements
Enhances
URL
Depends On Me
Imports Me
Suggests Me
Build Report

Package Archives

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

Package Source MEDIPS_1.20.1.tar.gz
Windows Binary MEDIPS_1.20.1.zip
Mac OS X 10.6 (Snow Leopard) MEDIPS_1.20.0.tgz
Mac OS X 10.9 (Mavericks) MEDIPS_1.20.1.tgz
Subversion source (username/password: readonly)
Git source https://github.com/Bioconductor-mirror/MEDIPS/tree/release-3.2
Package Short Url http://bioconductor.org/packages/MEDIPS/
Package Downloads Report Download Stats

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