MEDIPS

DOI: 10.18129/B9.bioc.MEDIPS  

DNA IP-seq data analysis

Bioconductor version: Release (3.16)

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 "4.2") 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")

 

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 1.50.0
In Bioconductor since BioC 2.7 (R-2.12) (12.5 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
Links To Me
Build Report  

Package Archives

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

Source Package MEDIPS_1.50.0.tar.gz
Windows Binary MEDIPS_1.50.0.zip
macOS Binary (x86_64) MEDIPS_1.50.0.tgz
macOS Binary (arm64) MEDIPS_1.50.0.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

Documentation »

Bioconductor

R / CRAN packages and documentation

Support »

Please read the posting guide. Post questions about Bioconductor to one of the following locations: