Files in paxtoolsr
PaxtoolsR: Access Pathways from Multiple Databases through BioPAX and Pathway Commons
.BBSoptions
.Rinstignore
NEWS
NAMESPACE
DESCRIPTION
build/vignette.rds
java/README.md
R/integrateBiopax.R
R/validate.R
R/readSbgn.R
R/downloadPc2.R
R/toGSEA.R
R/traverse.R
R/checkInputFile.R
R/downloadSignedPC.R
R/fetch.R
R/splitSifnxByPathway.R
R/mergeBiopax.R
R/checkInputFilePc.R
R/summarizeSif.R
R/fromPsimi.R
R/readSif.R
R/toLevel3.R
R/pcFormats.R
R/getSifInteractionCategories.R
R/loadSifInIgraph.R
R/getErrorMessage.R
R/pcGraphQueries.R
R/toSifnx.R
R/readBiopax.R
R/graphPc.R
R/toCytoscape.R
R/addAttributeList.R
R/getCacheFiles.R
R/downloadFile.R
R/toSBGN.R
R/convertSifToGmt.R
R/checkOutputFile.R
R/searchListOfVectors.R
R/getPcUrl.R
R/readPcPathwaysInfo.R
R/pcDirections.R
R/getPcRequest.R
R/mapValues.R
R/getPc.R
R/processPcRequest.R
R/topPathways.R
R/toSif.R
R/searchPc.R
R/convertDataFrameListsToVectors.R
R/convertSifToSpia.R
R/summarize.R
R/readGmt.R
R/filterSif.R
R/readSifnx.R
R/getNeighbors.R
R/getShortestPathSif.R
R/paxtoolsr.R
R/downloadPc.R
R/getPcDatabaseNames.R
vignettes/extract_pathways.R
vignettes/using_paxtoolsr.Rmd
vignettes/getNeighbors.R
man/summarize.Rd
man/pcFormats.Rd
man/topPathways.Rd
man/getNeighbors.Rd
man/toGSEA.Rd
man/downloadPc2.Rd
man/readSif.Rd
man/toSifnx.Rd
man/downloadSignedPC.Rd
man/convertSifToGmt.Rd
man/toSBGN.Rd
man/readGmt.Rd
man/getCacheFiles.Rd
man/mergeBiopax.Rd
man/processPcRequest.Rd
man/readSbgn.Rd
man/splitSifnxByPathway.Rd
man/loadSifInIgraph.Rd
man/toSif.Rd
man/readBiopax.Rd
man/validate.Rd
man/getPcUrl.Rd
man/toLevel3.Rd
man/downloadFile.Rd
man/traverse.Rd
man/addAttributeList.Rd
man/readSifnx.Rd
man/getShortestPathSif.Rd
man/pcGraphQueries.Rd
man/graphPc.Rd
man/getErrorMessage.Rd
man/pcDirections.Rd
man/mapAttributes.Rd
man/getSifInteractionCategories.Rd
man/searchListOfVectors.Rd
man/toCytoscape.Rd
man/filterSif.Rd
man/integrateBiopax.Rd
man/mapValues.Rd
man/summarizeSif.Rd
man/searchPc.Rd
man/fetch.Rd
man/readPcPathwaysInfo.Rd
man/getPcDatabaseNames.Rd
man/convertDataFrameListsToVectors.Rd
man/getPc.Rd
tests/testthat.R
tests/runTests.old
tests/testthat/test_pathwayCommons.R
tests/testthat/test_paxtools.R
inst/CITATION
inst/paxtoolsNotes.txt
inst/doc/using_paxtoolsr.R
inst/doc/using_paxtoolsr.Rmd
inst/doc/using_paxtoolsr.html
inst/ignore/convertToDF.R
inst/ignore/convertToDataFrameWithListOfVectors.R
inst/ignore/convertToPathwayList.R
inst/ignore/readSifnxSmall.R
inst/ignore/del.txt
inst/ignore/extractIds.R
inst/ignore/convertIds.R
inst/ignore/convertSifnxIds.R
inst/ignore/convertToDT.R
inst/java/paxtools-4.3.1.jar
inst/extdata/sif_color_code.txt
inst/extdata/test_gsea_1.gmt
inst/extdata/test_gsea.gmt
inst/extdata/test_sifnx_250.txt
inst/extdata/raf_map_kinase_cascade_reactome.owl
inst/extdata/test_PathwayCommons12.kegg.hgnc.gmt
inst/extdata/test_sifnx2.txt
inst/extdata/pathways.txt.gz
inst/extdata/test_edgelist.txt
inst/extdata/test_sifnx.txt
inst/extdata/dna_replication.owl
inst/extdata/test_sifnx_sm.txt
inst/extdata/test_sif.txt
inst/extdata/test_sif_shortestPath.txt
inst/extdata/10523676-compact.xml
inst/extdata/test_biopax.owl
inst/extdata/biopax3-short-metabolic-pathway.owl
inst/extdata/test_PathwayCommons12.netpath.hgnc.gmt
inst/extdata/REACT_12034-3.owl
inst/extdata/tca_cycle.sif
inst/extdata/test_sbgn.xml
