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methimpute

This is the development version of methimpute; for the stable release version, see methimpute.

Imputation-guided re-construction of complete methylomes from WGBS data

Bioconductor version: Development (3.18)

This package implements functions for calling methylation for all cytosines in the genome.

Author: Aaron Taudt

Maintainer: Aaron Taudt <aaron.taudt at gmail.com>

Citation (from within R, enter citation("methimpute")):

Installation

To install this package, start R (version "4.3") and enter: 

if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

# The following initializes usage of Bioc devel
BiocManager::install(version='devel')

BiocManager::install("methimpute")

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("methimpute")
Methylation status calling with METHimpute PDF R Script
Reference Manual PDF
NEWS Text

Details

biocViews Coverage, DNAMethylation, Epigenetics, HiddenMarkovModel, ImmunoOncology, Sequencing, Software
Version 1.23.0
In Bioconductor since BioC 3.6 (R-3.4) (6 years)
License Artistic-2.0
Depends R (>= 3.5.0), GenomicRanges, ggplot2
Imports Rcpp (>= 0.12.4.5), methods, utils, grDevices, stats, GenomeInfoDb, IRanges, Biostrings, reshape2, minpack.lm, data.table
Linking To Rcpp
Suggests knitr, BiocStyle
System Requirements
Enhances
URL
See More
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report  

Package Archives

Follow Installation instructions to use this package in your R session.

Source Package methimpute_1.23.0.tar.gz
Windows Binary methimpute_1.23.0.zip
macOS Binary (x86_64) methimpute_1.23.0.tgz
macOS Binary (arm64) methimpute_1.23.0.tgz
Source Repository git clone https://git.bioconductor.org/packages/methimpute
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/methimpute
Bioc Package Browser https://code.bioconductor.org/browse/methimpute/
Package Short Url https://bioconductor.org/packages/methimpute/
Package Downloads Report Download Stats