methimpute

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

All versions

3.24 (devel), 3.23 (release), 3.22, 3.21, 3.20, 3.19, 3.18, 3.17, 3.16, 3.15, 3.14, 3.13, 3.12, 3.11, 3.10, 3.9, 3.8, 3.7, 3.6

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

Bioconductor version: Development (3.24)

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")):

Aaron Taudt. methimpute: Imputation-guided re-construction of complete methylomes from WGBS data. doi:10.18129/B9.bioc.methimpute, R package version 1.35.0, https://bioconductor.org/packages/methimpute.

Generated from the package metadata; it may differ from the package's own citation.

Installation

To install this package, start R (version "4.6") and enter:

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

## The following initializes the development version of Bioconductor
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

Need some help? Ask on the Bioconductor Support site!

Details

biocViews	Coverage, DNAMethylation, Epigenetics, HiddenMarkovModel, ImmunoOncology, Sequencing, Software
Version	1.35.0
In Bioconductor since	BioC 3.6 (R-3.4) (9 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
URL

Suggests	knitr, BiocStyle
Linking To	Rcpp
Enhances
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report	Build Report, r-universe

Package Archives

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

Source Package	methimpute_1.35.0.tar.gz
Windows Binary (x86_64)	methimpute_1.35.0.zip
macOS Binary (big-sur-x86_64)	methimpute_1.35.0.tgz
macOS Binary (sonoma-arm64)	methimpute_1.35.0.tgz
Source Repository	git clone https://git.bioconductor.org/packages/methimpute
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/methimpute
Package Short Url	https://bioconductor.org/packages/methimpute/
Package Downloads Report	Download Stats