SIMD
This package is for version 3.10 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: 3.10
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 "3.6") 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 | ||
| NEWS | Text |
Details
| biocViews | DifferentialExpression, DifferentialMethylation, ImmunoOncology, SingleCell, Software |
| Version | 1.4.0 |
| 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 |
| System Requirements | |
| URL |
See More
| Suggests | BiocStyle, knitr, rmarkdown |
| Linking To | |
| Enhances | |
| Depends On Me | |
| Imports Me | |
| Suggests Me | |
| Links To Me | |
| Build Report | Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | SIMD_1.4.0.tar.gz |
| Windows Binary | SIMD_1.4.0.zip |
| Mac OS X 10.11 (El Capitan) | SIMD_1.4.0.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 |
| Old Source Packages for BioC 3.10 | Source Archive |