To install this package, start R and enter:

## try http:// if https:// URLs are not supported
source("https://bioconductor.org/biocLite.R")
biocLite("DEsubs")

In most cases, you don't need to download the package archive at all.

DEsubs

 

   

DEsubs: an R package for flexible identification of differentially expressed subpathways using RNA-seq expression experiments

Bioconductor version: Release (3.5)

DEsubs is a network-based systems biology package that extracts disease-perturbed subpathways within a pathway network as recorded by RNA-seq experiments. It contains an extensive and customizable framework covering a broad range of operation modes at all stages of the subpathway analysis, enabling a case-specific approach. The operation modes refer to the pathway network construction and processing, the subpathway extraction, visualization and enrichment analysis with regard to various biological and pharmacological features. Its capabilities render it a tool-guide for both the modeler and experimentalist for the identification of more robust systems-level biomarkers for complex diseases.

Author: Aristidis G. Vrahatis and Panos Balomenos

Maintainer: Aristidis G. Vrahatis <agvrahatis at upatras.gr> and Panos Balomenos <balomenos at upatras.gr>

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

Installation

To install this package, start R and enter:

## try http:// if https:// URLs are not supported
source("https://bioconductor.org/biocLite.R")
biocLite("DEsubs")

Documentation

To view documentation for the version of this package installed in your system, start R and enter:

browseVignettes("DEsubs")

 

PDF R Script DEsubs
PDF   Reference Manual
Text   NEWS

Details

biocViews DifferentialExpression, GeneExpression, GraphAndNetwork, KEGG, Network, NetworkEnrichment, Normalization, Pathways, RNASeq, Software, SystemsBiology
Version 1.2.1
In Bioconductor since BioC 3.4 (R-3.3) (0.5 years)
License GPL-3
Depends R (>= 3.3), locfit
Imports graph, igraph, RBGL, circlize, limma, edgeR, samr, EBSeq, NBPSeq, DESeq, stats, grDevices, graphics, pheatmap, utils, ggplot2, Matrix, jsonlite, tools, DESeq2, methods
LinkingTo
Suggests RUnit, BiocGenerics, 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.

Package Source DEsubs_1.2.1.tar.gz
Windows Binary DEsubs_1.2.1.zip
Mac OS X 10.11 (El Capitan) DEsubs_1.2.1.tgz
Subversion source (username/password: readonly)
Git source https://github.com/Bioconductor-mirror/DEsubs/tree/release-3.5
Package Short Url http://bioconductor.org/packages/DEsubs/
Package Downloads Report Download Stats

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