MEDIPS
This package is for version 3.12 of Bioconductor; for the stable, up-to-date release version, see MEDIPS.
DNA IP-seq data analysis
Bioconductor version: 3.12
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("MEDIPS")):
Installation
To install this package, start R (version "4.0") 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 | R Script | |
| Reference Manual |
Details
| biocViews | ChIPSeq, CopyNumberVariation, Coverage, CpGIsland, DNAMethylation, DifferentialExpression, Genetics, GenomeAnnotation, Microarray, Preprocessing, QualityControl, SequenceMatching, Sequencing, Software, Visualization |
| Version | 1.42.0 |
| 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 |
| 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_1.42.0.tar.gz |
| Windows Binary | MEDIPS_1.42.0.zip |
| macOS 10.13 (High Sierra) | MEDIPS_1.42.0.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 3.12 | Source Archive |