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Showing content from https://bioconductor.org/packages/devel/bioc/html/../../bioc/html/../../bioc/html/MEDIPS.html below:

Bioconductor - MEDIPS (development version)

MEDIPS

This is the development version of MEDIPS; for the stable release version, see MEDIPS.

DNA IP-seq data analysis

Bioconductor version: Development (3.22)

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 "4.5") and enter:


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

# The following initializes usage of Bioc devel
BiocManager::install(version='devel')

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")
Details biocViews ChIPSeq, CopyNumberVariation, Coverage, CpGIsland, DNAMethylation, DifferentialExpression, Genetics, GenomeAnnotation, Microarray, Preprocessing, QualityControl, SequenceMatching, Sequencing, Software, Visualization Version 1.61.0 In Bioconductor since BioC 2.7 (R-2.12) (14.5 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 Package Archives

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

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