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

Pathway-based data integration of omics data

Bioconductor version: Release (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>

Maintainer: Torsten Schoeps <torsten.schoeps at>

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


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

if (!require("BiocManager", quietly = TRUE))


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


Reference Manual PDF


biocViews GeneSignaling, GeneTarget, Software, SystemsBiology, Transcription
Version 1.36.0
In Bioconductor since BioC 3.1 (R-3.2) (9.5 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
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Suggests ebdbNet, longitudinal, Mfuzz, RUnit
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Source Package pwOmics_1.36.0.tar.gz
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