MEDIPS
DNA IP-seq data analysis
Bioconductor version: 3.23 · Package version: 1.64.0
Other Bioconductor versions
devel is the development version; release is the current stable one.
3.24 (devel), 3.23 (release)
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.
Installation
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("MEDIPS")Details
| Maintainer | Lukas Chavez <lukaschavez@ucsd.edu> |
| Author | Lukas Chavez, Matthias Lienhard, Joern Dietrich, Isaac Lopez Moyado |
| License | GPL (>=2) |
| Source branch | RELEASE_3_23 |
| Build report | Bioconductor build system, r-universe |
| biocViews | ChIPSeq, CopyNumberVariation, Coverage, CpGIsland, DNAMethylation, DifferentialExpression, Genetics, GenomeAnnotation, Microarray, Preprocessing, QualityControl, SequenceMatching, Sequencing, Software, Visualization |
| Package Short Url | https://bioconductor.org/packages/MEDIPS/ |
Citation
From within R, enter citation("MEDIPS"):
Lukas Chavez, Matthias Lienhard, Joern Dietrich, Isaac Lopez Moyado. MEDIPS: DNA IP-seq data analysis. doi:10.18129/B9.bioc.MEDIPS, R package version 1.64.0, https://bioconductor.org/packages/MEDIPS.
Generated from the package metadata; it may differ from the package's own citation.
Documentation
Download
Follow the installation instructions to use this package in your R session.
| Source package | MEDIPS_1.64.0.tar.gz |
| Windows binary (x86_64) | MEDIPS_1.64.0.zip |
| macOS binary (arm64) | MEDIPS_1.64.0.tgz |
| macOS binary (x86_64) | MEDIPS_1.64.0.tgz |
Dependencies
Depends: R (>= 3.0), BSgenome, Rsamtools
Imports: GenomicRanges, Biostrings, graphics, gtools, IRanges, methods, stats, utils, edgeR, DNAcopy, biomaRt, rtracklayer, preprocessCore
Suggests: BSgenome.Hsapiens.UCSC.hg19, MEDIPSData, BiocStyle