DEsubs
This package is for version 3.6 of Bioconductor; for the stable, up-to-date release version, see DEsubs.
DEsubs: an R package for flexible identification of differentially expressed subpathways using RNA-seq expression experiments
Bioconductor version: 3.6
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>, Panos Balomenos <balomenos at upatras.gr>
citation("DEsubs")):
Installation
To install this package, start R (version "3.4") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("DEsubs")
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("DEsubs")| DEsubs | R Script | |
| Reference Manual | ||
| NEWS | Text |
Details
| biocViews | DifferentialExpression, GeneExpression, GraphAndNetwork, KEGG, Network, NetworkEnrichment, Normalization, Pathways, RNASeq, Software, SystemsBiology |
| Version | 1.4.0 |
| In Bioconductor since | BioC 3.4 (R-3.3) (7.5 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 |
| System Requirements | |
| URL |
See More
| Suggests | RUnit, BiocGenerics, knitr |
| Linking To | |
| 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 | DEsubs_1.4.0.tar.gz |
| Windows Binary | DEsubs_1.4.0.zip |
| Mac OS X 10.11 (El Capitan) | DEsubs_1.4.0.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/DEsubs |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/DEsubs |
| Package Short Url | https://bioconductor.org/packages/DEsubs/ |
| Package Downloads Report | Download Stats |
| Old Source Packages for BioC 3.6 | Source Archive |