DEComplexDisease

DOI: 10.18129/B9.bioc.DEComplexDisease  

This package is deprecated. It will probably be removed from Bioconductor. Please refer to the package end-of-life guidelines for more information.

This package is for version 3.16 of Bioconductor. This package has been removed from Bioconductor. For the last stable, up-to-date release version, see DEComplexDisease.

A tool for differential expression analysis and DEGs based investigation to complex diseases by bi-clustering analysis

Bioconductor version: 3.16

It is designed to find the differential expressed genes (DEGs) for complex disease, which is characterized by the heterogeneous genomic expression profiles. Different from the established DEG analysis tools, it does not assume the patients of complex diseases to share the common DEGs. By applying a bi-clustering algorithm, DECD finds the DEGs shared by as many patients. In this way, DECD describes the DEGs of complex disease in a novel syntax, e.g. a gene list composed of 200 genes are differentially expressed in 30% percent of studied complex disease. Applying the DECD analysis results, users are possible to find the patients affected by the same mechanism based on the shared signatures.

Author: Guofeng Meng

Maintainer: Guofeng Meng <menggf at gmail.com>

Installation

To install this package, start R (version "4.2") and enter:

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

BiocManager::install("DEComplexDisease")

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("DEComplexDisease")

 

PDF		DEComplexDisease: a R package for DE analysis
HTML	R Script	DEComplexDisease: a R package for DE analysis
PDF		Reference Manual
Text		NEWS

Details

biocViews	Clustering, DNASeq, DifferentialExpression, FunctionalGenomics, GeneExpression, Software, WholeGenome
Version	1.18.0
In Bioconductor since	BioC 3.7 (R-3.5) (5 years)
License	GPL-3
Depends	R (>= 3.3.3)
Imports	Rcpp (>= 0.12.7), DESeq2, edgeR, SummarizedExperiment, ComplexHeatmap, grid, parallel, BiocParallel, grDevices, graphics, stats, methods, utils
LinkingTo	Rcpp
Suggests	knitr
SystemRequirements
Enhances
URL
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report

Package Archives

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

Source Package	DEComplexDisease_1.18.0.tar.gz
Windows Binary	DEComplexDisease_1.18.0.zip (64-bit only)
macOS Binary (x86_64)	DEComplexDisease_1.18.0.tgz
macOS Binary (arm64)	DEComplexDisease_1.18.0.tgz
Source Repository	git clone https://git.bioconductor.org/packages/DEComplexDisease
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/DEComplexDisease
Package Short Url	https://bioconductor.org/packages/DEComplexDisease/
Package Downloads Report	Download Stats