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This package is for version 3.2 of Bioconductor;
for the stable, up-to-date release version, see
MEDIPS.
DNA IP-seq data analysis
Bioconductor version: 3.2
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 <l.chavez at dkfz.de>
Citation (from within R,
enter citation("MEDIPS")
):
Installation
To install this package, start R and enter:
## try http:// if https:// URLs are not supported source("https://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")
MEDIPS | ||
Reference Manual |
Details
biocViews | ChIPSeq, CopyNumberVariation, Coverage, CpGIsland, DNAMethylation, DifferentialExpression, Genetics, GenomeAnnotation, Microarray, Preprocessing, QualityControl, SequenceMatching, Sequencing, Software, Visualization |
Version | 1.20.1 |
In Bioconductor since | BioC 2.7 (R-2.12) (5.5 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
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Installation instructions to use this
package in your R session.
Read more here: Source link