Files in MarenS2/pwOmics_maren
Pathway-based data integration of omics data
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DESCRIPTION
NAMESPACE
NEWS
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
data/OmicsExampleData.RData
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/provided_TF_genes.txt
inst/unitTests/pwIntOmics_exported.R
inst/unitTests/pwIntOmics_internal.R
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/infoConsensusGraph.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
pwOmics.Rproj
tests/runTests.R
vignettes/ConsensusGraphs_tp1.pdf
vignettes/ConsensusGraphs_tp24.pdf
vignettes/TempCorr_MAPK14_downstream.pdf
vignettes/TimeProfiles.pdf
vignettes/dynConsensusNet_2.pdf
vignettes/pwOmics.Rnw
vignettes/pwOmics_vignette.bib
vignettes/references.bib
vignettes/updown.pdf
