MEB
This is the development version of MEB; for the stable release version, see MEB.
A normalization-invariant minimum enclosing ball method to detect differentially expressed genes for RNA-seq and scRNA-seq data
DOI: 10.18129/B9.bioc.MEB
Bioconductor version: Development (3.24)
This package provides a method to identify differential expression genes in the same or different species. Given that non-DE genes have some similarities in features, a scaling-free minimum enclosing ball (SFMEB) model is built to cover those non-DE genes in feature space, then those DE genes, which are enormously different from non-DE genes, being regarded as outliers and rejected outside the ball. The method on this package is described in the article 'A minimum enclosing ball method to detect differential expression genes for RNA-seq data'. The SFMEB method is extended to the scMEB method that considering two or more potential types of cells or unknown labels scRNA-seq dataset DEGs identification.
Author: Yan Zhou, Jiadi Zhu
Maintainer: Jiadi Zhu <2160090406 at email.szu.edu.cn>, Yan Zhou <zhouy1016 at szu.edu.cn>
citation("MEB")):
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")
## The following initializes the development version of Bioconductor
BiocManager::install(version = "devel")
BiocManager::install("MEB")
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("MEB")| MEB Tutorial | HTML | R Script |
| Reference Manual | ||
| NEWS | Text |
Details
| biocViews | Classification, DifferentialExpression, GeneExpression, Normalization, Sequencing, Software |
| Version | 1.27.0 |
| In Bioconductor since | BioC 3.10 (R-3.6) (7 years) |
| License | GPL-2 |
| Depends | R (>= 3.6.0) |
| Imports | e1071, edgeR, scater, stats, wrswoR, SummarizedExperiment, SingleCellExperiment |
| System Requirements | |
| URL |
See More
| Suggests | knitr, rmarkdown, BiocStyle |
| 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 | MEB_1.27.0.tar.gz |
| Windows Binary (x86_64) | MEB_1.27.0.zip |
| macOS Binary (big-sur-x86_64) | MEB_1.27.0.tgz |
| macOS Binary (sonoma-arm64) | MEB_1.27.0.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/MEB |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/MEB |
| Bioc Package Browser | https://code.bioconductor.org/browse/MEB/ |
| Package Short Url | https://bioconductor.org/packages/MEB/ |
| Package Downloads Report | Download Stats |