methimpute

DOI: 10.18129/B9.bioc.methimpute    

This package is for version 3.9 of Bioconductor; for the stable, up-to-date release version, see methimpute.

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

Bioconductor version: 3.9

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

Author: Aaron Taudt

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

Installation

To install this package, start R (version "3.6") and enter:

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

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")

 

PDF	R Script	Methylation status calling with METHimpute
PDF		Reference Manual
Text		NEWS

Details

biocViews	Coverage, DNAMethylation, Epigenetics, HiddenMarkovModel, ImmunoOncology, Sequencing, Software
Version	1.6.0
In Bioconductor since	BioC 3.6 (R-3.4) (2 years)
License	Artistic-2.0
Depends	R (>= 3.4.0), GenomicRanges, ggplot2
Imports	Rcpp (>= 0.12.4.5), methods, utils, grDevices, stats, GenomeInfoDb, IRanges, Biostrings, reshape2, minpack.lm, data.table
LinkingTo	Rcpp
Suggests	knitr, BiocStyle
SystemRequirements
Enhances
URL
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_1.6.0.tar.gz
Windows Binary	methimpute_1.6.0.zip
Mac OS X 10.11 (El Capitan)	methimpute_1.6.0.tgz
Source Repository	git clone https://git.bioconductor.org/packages/methimpute
Source Repository (Developer Access)	git clone [email protected]:packages/methimpute
Package Short Url	https://bioconductor.org/packages/methimpute/
Package Downloads Report	Download Stats