pwOmics

DOI: 10.18129/B9.bioc.pwOmics    

This package is for version 3.13 of Bioconductor; for the stable, up-to-date release version, see pwOmics.

Pathway-based data integration of omics data

Bioconductor version: 3.13

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: Maren Sitte <Maren.Sitte at med.uni-goettingen.de>

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

Installation

To install this package, start R (version "4.1") and enter:

if (!requireNamespace("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

BiocManager::install("pwOmics")

For older versions of R, please refer to the appropriate Bioconductor release.

Documentation

PDF   Reference Manual
Text   NEWS

Details

biocViews GeneSignaling, GeneTarget, Software, SystemsBiology, Transcription
Version 1.24.0
In Bioconductor since BioC 3.1 (R-3.2) (6.5 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
Links To Me
Build Report  

Package Archives

Follow Installation instructions to use this package in your R session.

Source Package pwOmics_1.24.0.tar.gz
Windows Binary pwOmics_1.24.0.zip (32- & 64-bit)
macOS 10.13 (High Sierra) pwOmics_1.24.0.tgz
Source Repository git clone https://git.bioconductor.org/packages/pwOmics
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/pwOmics
Package Short Url https://bioconductor.org/packages/pwOmics/
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