methylPipe
This is the development version of methylPipe; for the stable release version, see methylPipe.
Base resolution DNA methylation data analysis
Bioconductor version: Development (3.20)
Memory efficient analysis of base resolution DNA methylation data in both the CpG and non-CpG sequence context. Integration of DNA methylation data derived from any methodology providing base- or low-resolution data.
Author: Mattia Pelizzola [aut], Kamal Kishore [aut], Mattia Furlan [ctb, cre]
Maintainer: Mattia Furlan <mattia.furlan at iit.it>
citation("methylPipe")):
Installation
To install this package, start R (version "4.4") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
# The following initializes usage of Bioc devel
BiocManager::install(version='devel')
BiocManager::install("methylPipe")
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("methylPipe")| methylPipe.pdf | R Script | |
| Reference Manual | ||
| NEWS | Text |
Details
| biocViews | Coverage, DNAMethylation, MethylSeq, Sequencing, Software |
| Version | 1.39.0 |
| In Bioconductor since | BioC 3.0 (R-3.1) (10 years) |
| License | GPL(>=2) |
| Depends | R (>= 3.5.0), methods, grDevices, graphics, stats, utils, GenomicRanges, SummarizedExperiment(>= 0.2.0), Rsamtools |
| Imports | marray, gplots, IRanges, BiocGenerics, Gviz, GenomicAlignments, Biostrings, parallel, data.table, GenomeInfoDb, S4Vectors |
| System Requirements | |
| URL |
See More
| Suggests | BSgenome.Hsapiens.UCSC.hg18, TxDb.Hsapiens.UCSC.hg18.knownGene, knitr, MethylSeekR |
| Linking To | |
| Enhances | |
| Depends On Me | ListerEtAlBSseq |
| Imports Me | compEpiTools |
| Suggests Me | |
| Links To Me | |
| Build Report | Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | methylPipe_1.39.0.tar.gz |
| Windows Binary (x86_64) | methylPipe_1.39.0.zip (64-bit only) |
| macOS Binary (x86_64) | methylPipe_1.39.0.tgz |
| macOS Binary (arm64) | methylPipe_1.39.0.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/methylPipe |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/methylPipe |
| Bioc Package Browser | https://code.bioconductor.org/browse/methylPipe/ |
| Package Short Url | https://bioconductor.org/packages/methylPipe/ |
| Package Downloads Report | Download Stats |