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

 

DNA IP-seq data analysis

Bioconductor version: Release (3.1)

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 <lchavez at liai.org>

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

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, CopyNumberVariation, Coverage, CpGIsland, DNAMethylation, DifferentialExpression, Genetics, GenomeAnnotation, Microarray, Preprocessing, QualityControl, SequenceMatching, Sequencing, Software, Visualization
Version 1.18.0
In Bioconductor since BioC 2.7 (R-2.12) (4.5 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_1.18.0.tar.gz
Windows Binary MEDIPS_1.18.0.zip
Mac OS X 10.6 (Snow Leopard) MEDIPS_1.18.0.tgz
Mac OS X 10.9 (Mavericks) MEDIPS_1.18.0.tgz
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