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 (3.16)

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 "4.2") and enter:

if (!require("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	1.16.0
In Bioconductor since	BioC 3.8 (R-3.5) (4.5 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
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Build Report

Package Archives

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

Source Package	SIMD_1.16.0.tar.gz
Windows Binary	SIMD_1.16.0.zip
macOS Binary (x86_64)	SIMD_1.16.0.tgz
macOS Binary (arm64)	SIMD_1.16.0.tgz
Source Repository	git clone https://git.bioconductor.org/packages/SIMD
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/SIMD
Bioc Package Browser	https://code.bioconductor.org/browse/SIMD/
Package Short Url	https://bioconductor.org/packages/SIMD/
Package Downloads Report	Download Stats