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
MarenS2/pwOmics_maren documentation built on Aug. 30, 2017, 12:41 a.m.