MEDIPS
This is thereleased version of MEDIPS; for the devel version, seeMEDIPS.
DNA IP-seq data analysis
Bioconductor version: Release (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("MEDIPS")):Installation
To install this package, start R (version "4.5") and enter:
if (!require("BiocManager", quietly = TRUE)) install.packages("BiocManager")BiocManager::install("MEDIPS")For older versions of R, please refer to the appropriateBioconductor 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 | 1.62.0 |
| In Bioconductor since | BioC 2.7 (R-2.12) (15 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 | MEDIPSData |
| Links To Me | |
| Build Report | Build Report |
Package Archives
FollowInstallation instructions to use this package in your R session.
| Source Package | MEDIPS_1.62.0.tar.gz |
| Windows Binary (x86_64) | MEDIPS_1.62.0.zip |
| macOS Binary (x86_64) | MEDIPS_1.62.0.tgz |
| macOS Binary (arm64) | MEDIPS_1.62.0.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 |