SIMD
This is the released version of SIMD; for the devel version, see SIMD.
Statistical Inferences with MeDIP-seq Data (SIMD) to infer the methylation level for each CpG site
Bioconductor version: Release (3.23)
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")):
Huber W, Carey VJ, Gentleman R, Anders S, Carlson M, Carvalho BS, Bravo HC, Davis S, Gatto L, Girke T, Gottardo R, Hahne F, Hansen KD, Irizarry RA, Lawrence M, Love MI, MacDonald J, Obenchain V, Oleś AK, Pagès H, Reyes A, Shannon P, Smyth GK, Tenenbaum D, Waldron L, Morgan M (2015). "Orchestrating high-throughput genomic analysis with Bioconductor." Nature Methods, 12(2), 115–121. doi:10.1038/nmeth.3252.
Gentleman RC, Carey VJ, Bates DM, Bolstad B, Dettling M, Dudoit S, Ellis B, Gautier L, Ge Y, Gentry J, Hornik K, Hothorn T, Huber W, Iacus S, Irizarry R, Leisch F, Li C, Maechler M, Rossini AJ, Sawitzki G, Smith C, Smyth G, Tierney L, Yang JYH, Zhang J (2004). "Bioconductor: open software development for computational biology and bioinformatics." Genome Biology, 5(10), R80. doi:10.1186/gb-2004-5-10-r80.
Installation
To install this package, start R (version "4.6") 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 | 1.30.0 |
| In Bioconductor since | BioC 3.8 (R-3.5) (8 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 | |
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| Build Report | Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | SIMD_1.30.0.tar.gz |
| Windows Binary (x86_64) | SIMD_1.30.0.zip (64-bit only) |
| macOS Binary (big-sur-x86_64) | SIMD_1.30.0.tgz |
| macOS Binary (sonoma-arm64) | SIMD_1.30.0.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 |