methylPipe
This package is for version 3.9 of Bioconductor; for the stable, up-to-date release version, see methylPipe.
Base resolution DNA methylation data analysis
Bioconductor version: 3.9
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: Kamal Kishore
Maintainer: Kamal Kishore <kamal.fartiyal84 at gmail.com>
citation("methylPipe")
):
Installation
To install this package, start R (version "3.6") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
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 | 1.18.0 |
In Bioconductor since | BioC 3.0 (R-3.1) (9.5 years) |
License | GPL(>=2) |
Depends | R (>= 3.2.0), 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_1.18.0.tar.gz |
Windows Binary | methylPipe_1.18.0.zip (32- & 64-bit) |
Mac OS X 10.11 (El Capitan) | methylPipe_1.18.0.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 |
Old Source Packages for BioC 3.9 | Source Archive |