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
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DEsubs: an R package for flexible identification of differentially expressed subpathways using RNA-seq expression experiments
Bioconductor version: Release (3.4)
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")
| R Script | DEsubs | |
| Reference Manual | ||
| Text | NEWS |
Details
| biocViews | DifferentialExpression, GeneExpression, GraphAndNetwork, KEGG, Network, NetworkEnrichment, Normalization, Pathways, RNASeq, Software, SystemsBiology |
| Version | 1.0.2 |
| 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_1.0.2.tar.gz |
| Windows Binary | DEsubs_1.0.2.zip |
| Mac OS X 10.9 (Mavericks) | DEsubs_1.0.2.tgz |
| Subversion source | (username/password: readonly) |
| Git source | https://github.com/Bioconductor-mirror/DEsubs/tree/release-3.4 |
| Package Short Url | http://bioconductor.org/packages/DEsubs/ |
| Package Downloads Report | Download Stats |
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