MEDIPS

This package is for version 3.9 of Bioconductor; for the stable, up-to-date release version, see MEDIPS.

DNA IP-seq data analysis

Bioconductor version: 3.9

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 <lukaschavez at ucsd.edu>

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

Installation

To install this package, start R (version "3.6") and enter:


if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

BiocManager::install("MEDIPS")

For older versions of R, please refer to the appropriate Bioconductor release.

Documentation

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

browseVignettes("MEDIPS")

MEDIPS	PDF	R Script
Reference Manual	PDF

Need some help? Ask on the Bioconductor Support site!

Details

biocViews	ChIPSeq, CopyNumberVariation, Coverage, CpGIsland, DNAMethylation, DifferentialExpression, Genetics, GenomeAnnotation, Microarray, Preprocessing, QualityControl, SequenceMatching, Sequencing, Software, Visualization
Version	1.36.0
In Bioconductor since	BioC 2.7 (R-2.12) (13.5 years)
License	GPL (>=2)
Depends	R (>= 3.0), BSgenome, Rsamtools
Imports	GenomicRanges, Biostrings, graphics, gtools, IRanges, methods, stats, utils, edgeR, DNAcopy, biomaRt, rtracklayer, preprocessCore
System Requirements
URL

Suggests	BSgenome.Hsapiens.UCSC.hg19, MEDIPSData, BiocStyle
Linking To
Enhances
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report	Build Report

Package Archives

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

Source Package	MEDIPS_1.36.0.tar.gz
Windows Binary	MEDIPS_1.36.0.zip
Mac OS X 10.11 (El Capitan)	MEDIPS_1.36.0.tgz
Source Repository	git clone https://git.bioconductor.org/packages/MEDIPS
Source Repository (Developer Access)	git clone [email protected]:packages/MEDIPS
Bioc Package Browser	https://code.bioconductor.org/browse/MEDIPS/
Package Short Url	https://bioconductor.org/packages/MEDIPS/
Package Downloads Report	Download Stats
Old Source Packages for BioC 3.9	Source Archive