MEDIPS

This package is for version 3.10 of Bioconductor; for the stable, up-to-date release version, see MEDIPS.

DNA IP-seq data analysis


Bioconductor version: 3.10

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

Details

biocViews ChIPSeq, CopyNumberVariation, Coverage, CpGIsland, DNAMethylation, DifferentialExpression, Genetics, GenomeAnnotation, Microarray, Preprocessing, QualityControl, SequenceMatching, Sequencing, Software, Visualization
Version 1.38.0
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
See More
Suggests BSgenome.Hsapiens.UCSC.hg19, MEDIPSData, BiocStyle
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Depends On Me
Imports Me
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Package Archives

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

Source Package MEDIPS_1.38.0.tar.gz
Windows Binary MEDIPS_1.38.0.zip
Mac OS X 10.11 (El Capitan) MEDIPS_1.38.0.tgz
Source Repository git clone https://git.bioconductor.org/packages/MEDIPS
Source Repository (Developer Access) git clone git@git.bioconductor.org: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 3.10 Source Archive