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

Bioconductor version: Development (3.19)

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 (from within R, enter citation("MEB")):

Installation

To install this package, start R (version "4.4") and enter:


if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

# The following initializes usage of Bioc devel
BiocManager::install(version='devel')

BiocManager::install("MEB")

For older versions of R, please refer to the appropriate Bioconductor release.

Documentation


Reference Manual	PDF

Need some help? Ask on the Bioconductor Support site!

Details

biocViews	Classification, DifferentialExpression, GeneExpression, Normalization, Sequencing, Software
Version	1.17.0
In Bioconductor since	BioC 3.10 (R-3.6) (4.5 years)
License	GPL-2
Depends	R (>= 3.6.0)
Imports	e1071, edgeR, scater, stats, wrswoR, SummarizedExperiment, SingleCellExperiment
System Requirements
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Suggests	knitr, rmarkdown, BiocStyle
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Package Archives

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

Source Package
Windows Binary
macOS Binary (x86_64)
macOS Binary (arm64)
Source Repository	git clone https://git.bioconductor.org/packages/MEB
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/MEB
Package Short Url	https://bioconductor.org/packages/MEB/
Package Downloads Report	Download Stats