pwOmics

DOI: 10.18129/B9.bioc.pwOmics  

Pathway-based data integration of omics data

Bioconductor version: Release (3.16)

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>

Installation

To install this package, start R (version "4.2") and enter:

if (!require("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	1.30.0
In Bioconductor since	BioC 3.1 (R-3.2) (8 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_1.30.0.tar.gz
Windows Binary	pwOmics_1.30.0.zip
macOS Binary (x86_64)	pwOmics_1.30.0.tgz
macOS Binary (arm64)	pwOmics_1.30.0.tgz
Source Repository	git clone https://git.bioconductor.org/packages/pwOmics
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/pwOmics
Bioc Package Browser	https://code.bioconductor.org/browse/pwOmics/
Package Short Url	https://bioconductor.org/packages/pwOmics/
Package Downloads Report	Download Stats