To install this package, start R and enter:

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

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

pwOmics

 

Pathway-based data integration of omics data

Bioconductor version: Release (3.5)

pwOmics performs pathway-based level-specific data comparison of matching omics data sets based on pre-analysed user-specified lists of differential genes/transcripts and phosphoproteins. A separate downstream analysis of phosphoproteomic data including pathway identification, transcription factor identification and target gene identification is opposed to the upstream analysis starting with gene or transcript information as basis for identification of upstream transcription factors and potential proteomic regulators. The cross-platform comparative analysis allows for comprehensive analysis of single time point experiments and time-series experiments by providing static and dynamic analysis tools for data integration. In addition, it provides functions to identify individual signaling axes based on data integration.

Author: Astrid Wachter <Astrid.Wachter at med.uni-goettingen.de>

Maintainer: Astrid Wachter <Astrid.Wachter at med.uni-goettingen.de>

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

Installation

To install this package, start R and enter:

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

Documentation

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

browseVignettes("pwOmics")

 

PDF R Script pwOmics
PDF   Reference Manual
Text   NEWS

Details

biocViews GeneSignaling, GeneTarget, Software, SystemsBiology, Transcription
Version 1.8.0
In Bioconductor since BioC 3.1 (R-3.2) (2.5 years)
License GPL (>= 2)
Depends R (>= 3.2)
Imports data.table, rBiopaxParser, igraph, STRINGdb, graphics, gplots, Biobase, BiocGenerics, AnnotationDbi, biomaRt, AnnotationHub, GenomicRanges, graph, grDevices, stats, utils
LinkingTo
Suggests ebdbNet, longitudinal, Mfuzz
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 pwOmics_1.8.0.tar.gz
Windows Binary pwOmics_1.8.0.zip
Mac OS X 10.11 (El Capitan) pwOmics_1.8.0.tgz
Source Repository git clone https://git.bioconductor.org/packages/pwOmics
Package Short Url http://bioconductor.org/packages/pwOmics/
Package Downloads Report Download Stats

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