DEComplexDisease
This package is for version 3.9 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: 3.9
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("DEComplexDisease")):
Installation
To install this package, start R (version "3.6") 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 | ||
| DEComplexDisease: a R package for DE analysis | HTML | R Script |
| Reference Manual | ||
| NEWS | Text |
Details
| biocViews | Clustering, DNASeq, DifferentialExpression, FunctionalGenomics, GeneExpression, Software, WholeGenome |
| Version | 1.4.0 |
| 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_1.4.0.tar.gz |
| Windows Binary | DEComplexDisease_1.4.0.zip |
| Mac OS X 10.11 (El Capitan) | DEComplexDisease_1.4.0.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/DEComplexDisease |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/DEComplexDisease |
| Bioc Package Browser | https://code.bioconductor.org/browse/DEComplexDisease/ |
| Package Short Url | https://bioconductor.org/packages/DEComplexDisease/ |
| Package Downloads Report | Download Stats |
| Old Source Packages for BioC 3.9 | Source Archive |