0865fa7f31af2d1a70383963d240d599 *DESCRIPTION
9cb245f3b6f827bc58d20e4ab8fb9997 *NAMESPACE
f94e729b11ce720e254aada440221ae7 *NEWS
218e431dac40dac7618cb3a4d3f9e362 *R/biopax2Classes.R
d2f54d7edb5174e206c3f48a04057c85 *R/downloadBiopaxData.R
3c167a0ad29b71c75b96130097c3675f *R/helperFunctions.R
cc74d99616bb5e3cf2ae06deceba4953 *R/modifyBiopax.R
c53a025130877143038f9eca5be3b0fa *R/parseBiopax.R
8994e7acf014bc168c77865bc9b8bcad *R/pathway2Graph.R
4e1a3e2ef8791de07e114bede3d17f6d *R/rBiopaxParser-package.R
421314642499dded71411e6b26f49e8b *R/selectBiopax.R
55b3c54591c4d9f2a3adc4651a4e67d8 *R/visualizeBiopax.R
09dd8c60bbbf6eb3d9b467d9be49bcfa *R/writeBiopax.R
ce94923daa9715c8a4b50d5d7480b129 *README.md
68d013586c6ae20ff0d04aacabba959a *build/vignette.rds
a2cacd4e504b743f3c2ae829a6199854 *data/biopaxLevel3Example.RData
4d457ce88c677a32d0a0d8b22d12c911 *data/biopaxexample.rda
83a2b6fc667d32a5b0f01e376e75189f *inst/CITATION
fc83c8bb8aa5184bee609c9c9dc9cbcd *inst/doc/rBiopaxParserVignette.R
37e55dab9d207fbe86b1cfb6395a81b8 *inst/doc/rBiopaxParserVignette.Rnw
515a25cdfbe90055ee3662274c1bd7ec *inst/doc/rBiopaxParserVignette.pdf
9557d3501e1f91229ccc5872088b192c *inst/unitTests/test_biopax2Classes.R
ca24da47dabac88d04f0321c80284c69 *inst/unitTests/test_downloadBiopaxData.R
98e65fb4ec6db14354f8dc92ea1013cc *inst/unitTests/test_helperFunctions.R
635318f734dabad5c4359502189f8896 *man/CLASS_INHERITANCE_BP2.Rd
34f20a02d844141bc694818bda3f818b *man/CLASS_INHERITANCE_BP3.Rd
80aa9c1fce1c18342b84084163e2d6fe *man/CLASS_PROPERTIES_BP2.Rd
d3f69d3f90d7b5cac77c501ba26961ba *man/CLASS_PROPERTIES_BP3.Rd
516b2c4406609556f102136832a94417 *man/DATABASE_BIOPAX.Rd
241774b34245d16c14c2a53290ed29c0 *man/addBiochemicalReaction.Rd
4a493b8a436ccdff56270617f9befc8b *man/addBiopaxInstance.Rd
40374b7a2abec69c52bd4e26e229cd9e *man/addBiopaxInstances.Rd
209ca9c8c50ca97312d166c4e5ecaf73 *man/addControl.Rd
1343351870d3a702b49deb20d1b6d008 *man/addPathway.Rd
1d58acb534549adbe1057adfa639b89b *man/addPathwayComponents.Rd
d7c887042425402a69e7f923c56ed672 *man/addPhysicalEntity.Rd
3627a22aafc5facc92220188bf4aa0ad *man/addPhysicalEntityParticipant.Rd
2c65f3915eb4eb0d39553af717c899ef *man/addPropertiesToBiopaxInstance.Rd
afa8e2be32b5428b4dd80011906d5207 *man/addhash.Rd
803acb81c0d64f83f64e75087904d71c *man/addns.Rd
0b7ed2065cadb6a3a469b834d0798952 *man/biopax.Rd
57c114aed2b46119b9556458f19c52be *man/calcGraphOverlap.Rd
f1ff97ceb72d355be268edea53217520 *man/checkValidity.Rd
e9d96b12c4f819579e7908630b6c43ce *man/colorGraphNodes.Rd
4089caae220fac6402675c49a7716aa2 *man/combineNodes.Rd
9f7f2a763d0a5a0a86cb087210ff195c *man/createBiopax.Rd
c2bffe96371b58eb84ff3bfe7caa769d *man/diffGraphs.Rd
398b8444aa31f381345335c0686629d2 *man/downloadBiopaxData.Rd
4a9280424d32c75f03122757bfabef03 *man/generateNewUniqueID.Rd
d04d9ce1553d5dc2fe56d2e0d847ef9d *man/getClassProperties.Rd
ec1e5b138cc5274383615fb496cdf188 *man/getInstanceClass.Rd
43557451db1abfe41fde34c110469929 *man/getInstanceProperty.Rd
76ca25e4228181547d8c8456b02b0eb4 *man/getNeighborhood.Rd
2bf35f5d84c195cc1e1dbdc649a39249 *man/getParticipants.Rd
730c38c34f1bbf054faa854ff1e81fe3 *man/getReferencedIDs.Rd
3ee49f7dba6458686a716cec9b805354 *man/getReferencingIDs.Rd
9b605fac4331cb95b2360601541155de *man/getSubClasses.Rd
ff3342313f36fbd682bb4eaa0e573587 *man/getSuperClasses.Rd
14cab5a390a3e8d2379b517b0b0c29ec *man/getXrefAnnotations.Rd
6ba31d45ecfef05f5507c2a5bef847bb *man/hasProperty.Rd
33dc7e138373f05cc9b9a8a425ee95cf *man/internal_NrOfXMLNodes.Rd
17ace011ea45f34748499ad4ca09d29f *man/internal_XMLInstance2DF.Rd
4004b0cde635719a06bd4e41538151ac *man/internal_checkArguments.Rd
9abd51ef95787913f2c20ca1d1b25198 *man/internal_generateXMLfromBiopax.Rd
dc16f0625dca25d0e6cacfd2c1d6fe27 *man/internal_getBiopaxModelAsDataFrame.Rd
979df861bfc4492ce7e77f309e52273e *man/internal_propertyListToDF.Rd
5b751c717ef53dca9fe26fe7bca0f1d5 *man/internal_resolvePhysicalEntityParticipant.Rd
671fbeaffa32553e6e237d5b76012630 *man/intersectGraphs.Rd
454e5456e50f21a210f8808f61cf702a *man/isOfClass.Rd
d024ce680db3af1dd093fbe59ca8dfa8 *man/isOfNamespace.Rd
ff6f289eca8718c43ef5d7564a71dbc1 *man/isURL.Rd
64b3f3d431df2c64d20609adb5bbe69e *man/layoutRegulatoryGraph.Rd
b2959f4c79d6b02667b9874c3a159689 *man/listComplexComponents.Rd
abf5210618ae45b61e819bae7a2add2e *man/listInstances.Rd
38194228d5209b46502ef1a0df403804 *man/listInteractionComponents.Rd
0d6f76c13608f688530795594b45e886 *man/listPathwayComponents.Rd
46f632700325a23201c85ee7cb5473b0 *man/listPathways.Rd
7dc89e1c4cf0233381768eaa80384ecb *man/mergePathways.Rd
1b193c410f605892ea293193ef2f61c3 *man/pathway2AdjacancyMatrix.Rd
d4c5ec05f6acfd27d8b7d620fb9916f2 *man/pathway2Geneset.Rd
997c937d2e784f96923bdc96e8f2e8c6 *man/pathway2Graph.Rd
e0e060595a41aa75de314a1d7bd7bc79 *man/pathway2RegulatoryGraph.Rd
58de51bc4c005ef828be942d50ef7b36 *man/plotRegulatoryGraph.Rd
5f8d3178be22ae0c28d82b4b9f878cb3 *man/print.biopax.Rd
0af0482a3d63db5c637d6bd48f75f309 *man/rBiopaxParser-package.Rd
6cf58c7a1dc10a9621b1d6448d0d843f *man/readBiopax.Rd
30e790d9723612a8ff4f6bed266b477f *man/removeDisconnectedParts.Rd
8f6c6d6c702396c1199d42ff3d63924a *man/removeInstance.Rd
3d93071ce9014f8f15b0e8a1218e2c0e *man/removeNodes.Rd
96c38c3bce2bc0ff24afd24937506446 *man/removeProperties.Rd
d487d5d9ab834d7f7f5cea2838642669 *man/selectInstances.Rd
554e10300cdd6b661b85d05d49ed910f *man/splitComplex.Rd
b39853ddbd3557f443ff74565b4a6d51 *man/striphash.Rd
618690f964aa168868000a2387c4e7bf *man/stripns.Rd
66f9219131eac864aa49824b0953b358 *man/transitiveClosure.Rd
bb7b47c5dcdff35ac8cb8d5c4ef62a02 *man/transitiveReduction.Rd
120deac5a59d92f71bd973179bdd5348 *man/unfactorize.Rd
582e256d4228d48117447264f2dd016b *man/uniteGraphs.Rd
fbd4ace53e5285f996c122f20b7cc8a1 *man/writeBiopax.Rd
8ead4b4957cec75b152c4cbe68f773d8 *tests/runTests.R
0ae0aacdec7e1c631fb5f9e27ea6b50c *vignettes/biopax2classgraph.pdf
813053558f7ad48d08b7cb91883079b1 *vignettes/biopaxsimple.pdf
f145ff9201d96b098a48befb2e82d0ad *vignettes/mergedpw.pdf
abc5e59bd8082932cf9001fb9fbaa770 *vignettes/newpathways2.png
37e55dab9d207fbe86b1cfb6395a81b8 *vignettes/rBiopaxParserVignette.Rnw
74a582b69f1379c286eb186acaa76734 *vignettes/segclock.pdf
8fba94b97ace98ae6bed2415fd3419a0 *vignettes/wntplot.pdf
