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pwOmics

This package is deprecated. It will probably be removed from Bioconductor. Please refer to the package end-of-life guidelines for more information.

This is the development version of pwOmics; for the stable release version, see pwOmics.

Pathway-based data integration of omics data


Bioconductor version: Development (3.19)

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: Torsten Schoeps <torsten.schoeps at bioinf.med.uni-goettingen.de>

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

Installation

To install this package, start R (version "4.4") and enter:


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

# The following initializes usage of Bioc devel
BiocManager::install(version='devel')

BiocManager::install("pwOmics")

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

Documentation

Reference Manual PDF
NEWS Text

Details

biocViews GeneSignaling, GeneTarget, Software, SystemsBiology, Transcription
Version 1.35.1
In Bioconductor since BioC 3.1 (R-3.2) (9 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
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Suggests ebdbNet, longitudinal, Mfuzz, RUnit
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Package Archives

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

Source Package pwOmics_1.35.1.tar.gz
Windows Binary pwOmics_1.35.1.zip (64-bit only)
macOS Binary (x86_64) pwOmics_1.35.1.tgz
macOS Binary (arm64) pwOmics_1.35.1.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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