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>

Citation (from within R, enter citation("DEComplexDisease")):

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

Details

biocViews Clustering, DNASeq, DifferentialExpression, FunctionalGenomics, GeneExpression, Software, WholeGenome
Version 1.18.0
In Bioconductor since BioC 3.7 (R-3.5) (6 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
System Requirements
URL
See More
Suggests knitr
Linking To Rcpp
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 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
Old Source Packages for BioC 3.16 Source Archive