SIMD

DOI: 10.18129/B9.bioc.SIMD    

Statistical Inferences with MeDIP-seq Data (SIMD) to infer the methylation level for each CpG site

Bioconductor version: Release (3.8)

This package provides a inferential analysis method for detecting differentially expressed CpG sites in MeDIP-seq data. It uses statistical framework and EM algorithm, to identify differentially expressed CpG sites. The methods on this package are described in the article 'Methylation-level Inferences and Detection of Differential Methylation with Medip-seq Data' by Yan Zhou, Jiadi Zhu, Mingtao Zhao, Baoxue Zhang, Chunfu Jiang and Xiyan Yang (2018, pending publication).

Author: Yan Zhou

Maintainer: Jiadi Zhu <2160090406 at email.szu.edu.cn>

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

Installation

To install this package, start R and enter:

if (!requireNamespace("BiocManager", quietly = TRUE))
    install.packages("BiocManager")
BiocManager::install("SIMD", version = "3.8")

Documentation

To view documentation for the version of this package installed in your system, start R and enter:

browseVignettes("SIMD")

 

HTML R Script SIMD Tutorial
PDF   Reference Manual
Text   NEWS

Details

biocViews DifferentialExpression, DifferentialMethylation, SingleCell, Software
Version 1.0.0
License GPL-3
Depends R (>= 3.5.0)
Imports edgeR, statmod, methylMnM, stats, utils
LinkingTo
Suggests BiocStyle, knitr, rmarkdown
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 SIMD_1.0.0.tar.gz
Windows Binary SIMD_1.0.0.zip (32- & 64-bit)
Mac OS X 10.11 (El Capitan) SIMD_1.0.0.tgz
Source Repository git clone https://git.bioconductor.org/packages/SIMD
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/SIMD
Package Short Url http://bioconductor.org/packages/SIMD/
Package Downloads Report Download Stats

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