MEDIPS
This is the development version of MEDIPS; for the stable release version, see MEDIPS.
DNA IP-seq data analysis
Bioconductor version: Development (3.24)
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")):
Huber W, Carey VJ, Gentleman R, Anders S, Carlson M, Carvalho BS, Bravo HC, Davis S, Gatto L, Girke T, Gottardo R, Hahne F, Hansen KD, Irizarry RA, Lawrence M, Love MI, MacDonald J, Obenchain V, Oleś AK, Pagès H, Reyes A, Shannon P, Smyth GK, Tenenbaum D, Waldron L, Morgan M (2015). "Orchestrating high-throughput genomic analysis with Bioconductor." Nature Methods, 12(2), 115–121. doi:10.1038/nmeth.3252.
Gentleman RC, Carey VJ, Bates DM, Bolstad B, Dettling M, Dudoit S, Ellis B, Gautier L, Ge Y, Gentry J, Hornik K, Hothorn T, Huber W, Iacus S, Irizarry R, Leisch F, Li C, Maechler M, Rossini AJ, Sawitzki G, Smith C, Smyth G, Tierney L, Yang JYH, Zhang J (2004). "Bioconductor: open software development for computational biology and bioinformatics." Genome Biology, 5(10), R80. doi:10.1186/gb-2004-5-10-r80.
Installation
To install this package, start R (version "4.6") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
## The following initializes the development version of Bioconductor
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")| MEDIPS | R Script | |
| Reference Manual |
Details
| biocViews | ChIPSeq, CopyNumberVariation, Coverage, CpGIsland, DNAMethylation, DifferentialExpression, Genetics, GenomeAnnotation, Microarray, Preprocessing, QualityControl, SequenceMatching, Sequencing, Software, Visualization |
| Version | 1.65.0 |
| In Bioconductor since | BioC 2.7 (R-2.12) (16 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 | decemedip |
| Suggests Me | MEDIPSData |
| Links To Me | |
| Build Report | Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | MEDIPS_1.65.0.tar.gz |
| Windows Binary (x86_64) | MEDIPS_1.65.0.zip |
| macOS Binary (big-sur-x86_64) | MEDIPS_1.65.0.tgz |
| macOS Binary (sonoma-arm64) | MEDIPS_1.65.0.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 |