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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 (3.19)

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 "4.4") 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 1.25.0
In Bioconductor since BioC 3.6 (R-3.4) (6.5 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
System Requirements
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Suggests knitr, BiocStyle
Linking To Rcpp
Enhances
Depends On Me
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Package Archives

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

Source Package methimpute_1.25.0.tar.gz
Windows Binary methimpute_1.25.0.zip
macOS Binary (x86_64) methimpute_1.25.0.tgz
macOS Binary (arm64) methimpute_1.25.0.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