pwOmics: Pathway-based data integration of omics data

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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 proteins. A separate downstream analysis of proteomic data including pathway identification and enrichment analysis, 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 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.

Author
Astrid Wachter <Astrid.Wachter@med.uni-goettingen.de>
Date of publication
None
Maintainer
Astrid Wachter <Astrid.Wachter@med.uni-goettingen.de>
License
GPL (>= 2)
Version
1.6.0

View on Bioconductor

Man pages

addFeedbackLoops
Add feedback loops from target genes to proteins/TFs if...
clusterTimeProfiles
Clustering of time profiles.
consDynamicNet
Dynamic analysis.
createBiopaxnew
Create a new Biopax model containing all database...
createIntIDs
Create internal IDs.
enrichPWs
Pathway enrichment - downstream analysis.
enrichTFs
Transcription factor enrichment - upstream analysis.
findxneighborsoverlap
Find overlap of next neighbors of transcription factors in...
findxnextneighbors
Find next neighbors of transcription factors in identified...
genfullConsensusGraph
Combine SteinerNet with bipartite graph to get full consensus...
genGenelists
Generate genelists from pathway databases.
genGenelistssub
Generate internally genelists from pathway databases.
genIntIDs
Internal function for generation of pathway database specific...
getAlias_Ensemble
Get Gene Symbols from Ensemble Gene Accession IDs.
getAliasfromSTRINGIDs
Map alias names to STRING IDs of consensus graph.
getBiopaxModel
Get upstream regulators of identified transcription factors.
getbipartitegraphInfo
Get TF-target gene information for the consensus graph.
getConsensusSTRINGIDs
Get consensus graph in STRING IDs.
getDS_PWs
Get downstream analysis pathways.
getDS_TFs
Get downstream analysis transcription factors in pathways.
getDS_TGs
Get downstream analysis target genes of TFs found in...
getFCsplines
Get fold change splines.
getGenesIntersection
Get genes intersection for the omics data on the different...
getOmicsallGeneIDs
Get all gene IDs.
getOmicsallProteinIDs
Get all protein IDs.
getOmicsDataset
Get Omics dataset.
getOmicsTimepoints
Get Omics timepoints.
getProteinIntersection
Get protein intersection for the omics data on the different...
getSTRING_graph
Generate STRING PPI graph.
getTFIntersection
Get TF intersection for the omics data on the different time...
gettpIntersection
Get omics data intersection on the three levels. Get...
getUS_PWs
Get upstream pathways of identified transcription factors.
getUS_regulators
Get upstream regulators of identified transcription factors.
getUS_TFs
Get upstream TFs.
identifyPWs
Identify pathway IDs and pathway names of differentially...
identifyPWTFTGs
Identify TFs in enriched pathways and their target genes -...
identifyRsofTFs
Identify regulators of enriched transcription factors -...
identifyTFs
Transcription factor identification.
identPWsofTFs
Identification of pathways containing the transcription...
identRegulators
Identify overlapping upstream regulators of x transcription...
identTFs
This function provides a data.table of upstream transcription...
identTFTGsinPWs
Prepare OmicsData object for pathway information.
loadGenelists
Loading of genelists
loadPWs
Load pathway database information.
OmicsExampleData
Omics example dataset.
plotConsDynNet
Plot inferred net based on analysis analysis.
plotConsensusGraph
Plot consensus graph(s) from static analysis.
plotConsensusProfiles
Plot consensus graph profiles of static consensus molecules.
plotTimeProfileClusters
Plot time profile clusters of dynamic analysis result.
predictFCvals
Prediction of continous data points via smoothing splines.
preparePWinfo
Prepare OmicsData object for pathway information.
print.OmicsData
Print an OmicsData object.
PWidentallprots
Identification of pathwayIDs and pathway names for all...
PWidentallprotssub
Internal subfunction for all protein pathway identification.
PWidenttps
Identification of pathwayIDs and pathway names for proteins...
pwIntOmics-package
Pathway-based data integration of omics data
readOmics
Read in omics data.
readPWdata
Read in pathway database data needed for pathway...
readTFdata
Reads in chosen transcription factor target database...
readTFtargets
Read in matching transcription factor target gene pairs.
selectPWsofTFs
Select pathways with more than x TFs
staticConsensusNet
Static analysis.
SteinerTree_cons
Steiner tree algorithm.
TFidentallgenes
Identification of upstream transcription factors for all...
TFidenttps
Identification of upstream transcription factors.

Files in this package

pwOmics/DESCRIPTION
pwOmics/NAMESPACE
pwOmics/NEWS
pwOmics/R
pwOmics/R/pwOmics_consensus_analysis.R
pwOmics/R/pwOmics_downstream_analysis.R
pwOmics/R/pwOmics_example_dataset.R
pwOmics/R/pwOmics_get_functions.R
pwOmics/R/pwOmics_helper_functions.R
pwOmics/R/pwOmics_print.R
pwOmics/R/pwOmics_read_data.R
pwOmics/R/pwOmics_time_profiles.R
pwOmics/R/pwOmics_upstream_analysis.R
pwOmics/R/pwOmics_vizualisation_functions.R
pwOmics/build
pwOmics/build/vignette.rds
pwOmics/data
pwOmics/data/OmicsExampleData.RData
pwOmics/inst
pwOmics/inst/doc
pwOmics/inst/doc/pwOmics.R
pwOmics/inst/doc/pwOmics.Rnw
pwOmics/inst/doc/pwOmics.pdf
pwOmics/inst/extdata
pwOmics/inst/extdata/Genelists
pwOmics/inst/extdata/Genelists/Genelist_biocarta.RData
pwOmics/inst/extdata/chea-background.csv
pwOmics/inst/unitTests
pwOmics/inst/unitTests/provided_TF_genes.txt
pwOmics/inst/unitTests/pwIntOmics_exported.R
pwOmics/inst/unitTests/pwIntOmics_internal.R
pwOmics/man
pwOmics/man/OmicsExampleData.Rd
pwOmics/man/PWidentallprots.Rd
pwOmics/man/PWidentallprotssub.Rd
pwOmics/man/PWidenttps.Rd
pwOmics/man/SteinerTree_cons.Rd
pwOmics/man/TFidentallgenes.Rd
pwOmics/man/TFidenttps.Rd
pwOmics/man/addFeedbackLoops.Rd
pwOmics/man/clusterTimeProfiles.Rd
pwOmics/man/consDynamicNet.Rd
pwOmics/man/createBiopaxnew.Rd
pwOmics/man/createIntIDs.Rd
pwOmics/man/enrichPWs.Rd
pwOmics/man/enrichTFs.Rd
pwOmics/man/findxneighborsoverlap.Rd
pwOmics/man/findxnextneighbors.Rd
pwOmics/man/genGenelists.Rd
pwOmics/man/genGenelistssub.Rd
pwOmics/man/genIntIDs.Rd
pwOmics/man/genfullConsensusGraph.Rd
pwOmics/man/getAlias_Ensemble.Rd
pwOmics/man/getAliasfromSTRINGIDs.Rd
pwOmics/man/getBiopaxModel.Rd
pwOmics/man/getConsensusSTRINGIDs.Rd
pwOmics/man/getDS_PWs.Rd
pwOmics/man/getDS_TFs.Rd
pwOmics/man/getDS_TGs.Rd
pwOmics/man/getFCsplines.Rd
pwOmics/man/getGenesIntersection.Rd
pwOmics/man/getOmicsDataset.Rd
pwOmics/man/getOmicsTimepoints.Rd
pwOmics/man/getOmicsallGeneIDs.Rd
pwOmics/man/getOmicsallProteinIDs.Rd
pwOmics/man/getProteinIntersection.Rd
pwOmics/man/getSTRING_graph.Rd
pwOmics/man/getTFIntersection.Rd
pwOmics/man/getUS_PWs.Rd
pwOmics/man/getUS_TFs.Rd
pwOmics/man/getUS_regulators.Rd
pwOmics/man/getbipartitegraphInfo.Rd
pwOmics/man/gettpIntersection.Rd
pwOmics/man/identPWsofTFs.Rd
pwOmics/man/identRegulators.Rd
pwOmics/man/identTFTGsinPWs.Rd
pwOmics/man/identTFs.Rd
pwOmics/man/identifyPWTFTGs.Rd
pwOmics/man/identifyPWs.Rd
pwOmics/man/identifyRsofTFs.Rd
pwOmics/man/identifyTFs.Rd
pwOmics/man/loadGenelists.Rd
pwOmics/man/loadPWs.Rd
pwOmics/man/plotConsDynNet.Rd
pwOmics/man/plotConsensusGraph.Rd
pwOmics/man/plotConsensusProfiles.Rd
pwOmics/man/plotTimeProfileClusters.Rd
pwOmics/man/predictFCvals.Rd
pwOmics/man/preparePWinfo.Rd
pwOmics/man/print.OmicsData.Rd
pwOmics/man/pwIntOmics-package.Rd
pwOmics/man/readOmics.Rd
pwOmics/man/readPWdata.Rd
pwOmics/man/readTFdata.Rd
pwOmics/man/readTFtargets.Rd
pwOmics/man/selectPWsofTFs.Rd
pwOmics/man/staticConsensusNet.Rd
pwOmics/tests
pwOmics/tests/runTests.R
pwOmics/vignettes
pwOmics/vignettes/ConsensusGraphs_1.pdf
pwOmics/vignettes/ConsensusGraphs_2.pdf
pwOmics/vignettes/TimeProfiles.pdf
pwOmics/vignettes/dynConsensusNet_2.pdf
pwOmics/vignettes/pwOmics.Rnw
pwOmics/vignettes/pwOmics_vignette.bib
pwOmics/vignettes/references.bib
pwOmics/vignettes/updown.pdf
pwOmics/vignettes/workflow.pdf