SIMD

DOI: 10.18129/B9.bioc.SIMD    

This package is for version 3.12 of Bioconductor; for the stable, up-to-date release version, see SIMD.

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

Bioconductor version: 3.12

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>

Installation

To install this package, start R (version "4.0") and enter:

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

BiocManager::install("SIMD")

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("SIMD")

 

HTML	R Script	SIMD Tutorial
PDF		Reference Manual
Text		NEWS

Details

biocViews	DifferentialExpression, DifferentialMethylation, ImmunoOncology, SingleCell, Software
Version	1.8.0
In Bioconductor since	BioC 3.8 (R-3.5) (2.5 years)
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_1.8.0.tar.gz
Windows Binary	SIMD_1.8.0.zip (32- & 64-bit)
macOS 10.13 (High Sierra)	SIMD_1.8.0.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	https://bioconductor.org/packages/SIMD/
Package Downloads Report	Download Stats