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SIMD

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


Bioconductor version: Release (3.18)

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 (version "4.3") 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")
SIMD Tutorial HTML R Script
Reference Manual PDF
NEWS Text

Details

biocViews DifferentialExpression, DifferentialMethylation, ImmunoOncology, SingleCell, Software
Version 1.20.0
In Bioconductor since BioC 3.8 (R-3.5) (5.5 years)
License GPL-3
Depends R (>= 3.5.0)
Imports edgeR, statmod, methylMnM, stats, utils
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Package Archives

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

Source Package SIMD_1.20.0.tar.gz
Windows Binary SIMD_1.20.0.zip
macOS Binary (x86_64) SIMD_1.20.0.tgz
macOS Binary (arm64) SIMD_1.20.0.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