DEComplexDisease

DOI: 10.18129/B9.bioc.DEComplexDisease    

This is the development version of DEComplexDisease; for the stable release version, see DEComplexDisease.

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

Bioconductor version: Development (3.8)

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 and enter:

## try http:// if https:// URLs are not supported
source("http://bioc.ism.ac.jp/biocLite.R")
biocLite("DEComplexDisease")

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 1.1.0
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
Build Report  

Package Archives

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

Source Package DEComplexDisease_1.1.0.tar.gz
Windows Binary DEComplexDisease_1.1.0.zip (32- & 64-bit)
Mac OS X 10.11 (El Capitan) DEComplexDisease_1.1.0.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 http://bioconductor.org/packages/DEComplexDisease/
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