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 package is for version 3.19 of Bioconductor. This package has been removed from Bioconductor. For the last stable, up-to-date release version, see pwOmics.
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 med.uni-goettingen.de>
Maintainer: Torsten Schoeps <torsten.schoeps at bioinf.med.uni-goettingen.de>
citation("pwOmics")):
Installation
To install this package, start R (version "4.4") 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
| Reference Manual | |
| NEWS | Text |
Details
| 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 |
| System Requirements | |
| URL |
See More
| Suggests | ebdbNet, longitudinal, Mfuzz, RUnit |
| Linking To | |
| Enhances | |
| Depends On Me | |
| Imports Me | |
| Suggests Me | |
| Links To Me | |
| Build Report | Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | pwOmics_1.36.0.tar.gz |
| Windows Binary (x86_64) | pwOmics_1.36.0.zip |
| macOS Binary (x86_64) | pwOmics_1.36.0.tgz |
| macOS Binary (arm64) | pwOmics_1.36.0.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/ |
| Package Downloads Report | Download Stats |