SIMD
This is thereleased version of SIMD; for the devel version, seeSIMD.
Statistical Inferences with MeDIP-seq Data (SIMD) to infer the methylation level for each CpG site
Bioconductor version: Release (3.22)
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("SIMD")):Installation
To install this package, start R (version "4.5") and enter:
if (!require("BiocManager", quietly = TRUE)) install.packages("BiocManager")BiocManager::install("SIMD")For older versions of R, please refer to the appropriateBioconductor 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 | ||
| NEWS | Text |
Details
| biocViews | DifferentialExpression,DifferentialMethylation,ImmunoOncology,SingleCell,Software |
| Version | 1.28.0 |
| In Bioconductor since | BioC 3.8 (R-3.5) (7 years) |
| License | GPL-3 |
| Depends | R (>= 3.5.0) |
| Imports | edgeR,statmod,methylMnM, stats, utils |
| System Requirements | |
| URL |
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| Suggests | BiocStyle,knitr,rmarkdown |
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| Build Report | Build Report |
Package Archives
FollowInstallation instructions to use this package in your R session.
| Source Package | SIMD_1.28.0.tar.gz |
| Windows Binary (x86_64) | SIMD_1.28.0.zip (64-bit only) |
| macOS Binary (x86_64) | SIMD_1.28.0.tgz |
| macOS Binary (arm64) | SIMD_1.28.0.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 |