pwOmics: Pathway-based data integration of omics data

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.

Install the latest version of this package by entering the following in R:
source("https://bioconductor.org/biocLite.R")
biocLite("pwOmics")
AuthorAstrid Wachter <Astrid.Wachter@med.uni-goettingen.de>
Bioconductor views GeneSignaling GeneTarget SystemsBiology Transcription
Date of publicationNone
MaintainerAstrid Wachter <Astrid.Wachter@med.uni-goettingen.de>
LicenseGPL (>= 2)
Version1.8.0

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.

findSignalingAxes: Find downstream signaling axis.

findxneighborsoverlap: Find overlap of next neighbors of transcription factors in...

findxnextneighbors: Find next neighbors of transcription factors in identified...

generate_DSSignalingBase: Generate a folder with downstream information about all...

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...

get_matching_transcripts: Summarize table of matching downstream transcripts.

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.

identifyPR: Identify phosphorylation regulation influence downstream

identifyPWs: Identify pathway IDs and pathway names of differentially...

identifyPWTFTGs: Identify TFs in pathways and their target genes - downstream...

identifyRsofTFs: Identify regulators of transcription factors - upstream...

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.

readPhosphodata: Reads in phosphoprotein downstream regulation information.

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.

temp_correlations: Plot temporal correlations of phosphoprotein expression...

TFidentallgenes: Identification of upstream transcription factors for all...

TFidenttps: Identification of upstream transcription factors.

Functions

addFeedbackLoops Man page
clusterTimeProfiles Man page
consDynamicNet Man page
createBiopaxnew Man page
createIntIDs Man page
findSignalingAxes Man page
findxneighborsoverlap Man page
findxnextneighbors Man page
generate_DSSignalingBase Man page
genfullConsensusGraph Man page
genGenelists Man page
genGenelistssub Man page
genIntIDs Man page
getAlias_Ensemble Man page
getAliasfromSTRINGIDs Man page
getBiopaxModel Man page
getbipartitegraphInfo Man page
getConsensusSTRINGIDs Man page
getDS_PWs Man page
getDS_TFs Man page
getDS_TGs Man page
getFCsplines Man page
getGenesIntersection Man page
get_matching_transcripts Man page
getOmicsallGeneIDs Man page
getOmicsallProteinIDs Man page
getOmicsDataset Man page
getOmicsTimepoints Man page
getProteinIntersection Man page
getSTRING_graph Man page
getTFIntersection Man page
gettpIntersection Man page
getUS_PWs Man page
getUS_regulators Man page
getUS_TFs Man page
identifyPR Man page
identifyPWs Man page
identifyPWTFTGs Man page
identifyRsofTFs Man page
identifyTFs Man page
identPWsofTFs Man page
identRegulators Man page
identTFs Man page
identTFTGsinPWs Man page
loadGenelists Man page
loadPWs Man page
OmicsExampleData Man page
plotConsDynNet Man page
plotConsensusGraph Man page
plotConsensusProfiles Man page
plotTimeProfileClusters Man page
predictFCvals Man page
preparePWinfo Man page
print.OmicsData Man page
PWidentallprots Man page
PWidentallprotssub Man page
PWidenttps Man page
pwIntOmics Man page
pwIntOmics-package Man page
readOmics Man page
readPhosphodata Man page
readPWdata Man page
readTFdata Man page
readTFtargets Man page
selectPWsofTFs Man page
staticConsensusNet Man page
SteinerTree_cons Man page
temp_correlations Man page
TFidentallgenes Man page
TFidenttps Man page

Files

DESCRIPTION
NAMESPACE
NEWS
R
R/pwOmics_consensus_analysis.R R/pwOmics_downstream_analysis.R R/pwOmics_example_dataset.R R/pwOmics_get_functions.R R/pwOmics_helper_functions.R R/pwOmics_integration_functions.R R/pwOmics_print.R R/pwOmics_read_data.R R/pwOmics_time_profiles.R R/pwOmics_upstream_analysis.R R/pwOmics_vizualisation_functions.R
build
build/vignette.rds
data
data/OmicsExampleData.RData
inst
inst/doc
inst/doc/pwOmics.R
inst/doc/pwOmics.Rnw
inst/doc/pwOmics.pdf
inst/extdata
inst/extdata/Genelists
inst/extdata/Genelists/Genelist_biocarta.RData
inst/extdata/Genelists/Genelist_kegg.RData
inst/extdata/Genelists/Genelist_nci.RData
inst/extdata/Genelists/Genelist_reactome.RData
inst/extdata/TF_targets.txt
inst/extdata/chea-background.csv
inst/extdata/mat_phospho.csv
inst/extdata/phospho_anno.txt
inst/extdata/phospho_reg_table.txt
inst/extdata/transcriptome_signif.txt
inst/unitTests
inst/unitTests/provided_TF_genes.txt
inst/unitTests/pwIntOmics_exported.R inst/unitTests/pwIntOmics_internal.R
man
man/OmicsExampleData.Rd man/PWidentallprots.Rd man/PWidentallprotssub.Rd man/PWidenttps.Rd man/SteinerTree_cons.Rd man/TFidentallgenes.Rd man/TFidenttps.Rd man/addFeedbackLoops.Rd man/clusterTimeProfiles.Rd man/consDynamicNet.Rd man/createBiopaxnew.Rd man/createIntIDs.Rd man/findSignalingAxes.Rd man/findxneighborsoverlap.Rd man/findxnextneighbors.Rd man/genGenelists.Rd man/genGenelistssub.Rd man/genIntIDs.Rd man/generate_DSSignalingBase.Rd man/genfullConsensusGraph.Rd man/getAlias_Ensemble.Rd man/getAliasfromSTRINGIDs.Rd man/getBiopaxModel.Rd man/getConsensusSTRINGIDs.Rd man/getDS_PWs.Rd man/getDS_TFs.Rd man/getDS_TGs.Rd man/getFCsplines.Rd man/getGenesIntersection.Rd man/getOmicsDataset.Rd man/getOmicsTimepoints.Rd man/getOmicsallGeneIDs.Rd man/getOmicsallProteinIDs.Rd man/getProteinIntersection.Rd man/getSTRING_graph.Rd man/getTFIntersection.Rd man/getUS_PWs.Rd man/getUS_TFs.Rd man/getUS_regulators.Rd man/get_matching_transcripts.Rd man/getbipartitegraphInfo.Rd man/gettpIntersection.Rd man/identPWsofTFs.Rd man/identRegulators.Rd man/identTFTGsinPWs.Rd man/identTFs.Rd man/identifyPR.Rd man/identifyPWTFTGs.Rd man/identifyPWs.Rd man/identifyRsofTFs.Rd man/identifyTFs.Rd man/loadGenelists.Rd man/loadPWs.Rd man/plotConsDynNet.Rd man/plotConsensusGraph.Rd man/plotConsensusProfiles.Rd man/plotTimeProfileClusters.Rd man/predictFCvals.Rd man/preparePWinfo.Rd man/print.OmicsData.Rd man/pwIntOmics-package.Rd man/readOmics.Rd man/readPWdata.Rd man/readPhosphodata.Rd man/readTFdata.Rd man/readTFtargets.Rd man/selectPWsofTFs.Rd man/staticConsensusNet.Rd man/temp_correlations.Rd
tests
tests/runTests.R
vignettes
vignettes/ConsensusGraphs_tp1.pdf
vignettes/ConsensusGraphs_tp24.pdf
vignettes/TempCorr_MAPK14_downstream.pdf
vignettes/TimeProfiles.pdf
vignettes/dynConsensusNet_2.pdf
vignettes/pwOmics.Rnw
vignettes/updown.pdf

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