Files in wind22zhu/BioMedR

Generating Various Molecular Representations for Chemicals, Proteins, DNAs, RNAs and Their Interactions

R/001-BioMedR-package.R R/1001-clusterMDS.R R/1002-clusterCMP.R R/1003-clusterJarvis-Patrick.R R/1004-clusterStat.R R/1006-clusterPlotSOMmap.R R/101-getDrug.R R/102-getProt.R R/103-getDNAGenbank.R R/1101-randomForest.R R/1102-PLS.R R/1103-rffs.R R/400-extractDrugAIO.R R/401-extractDrugALOGP.R R/404-extractDrugAminoAcidCount.R R/408-extractDrugAutocorrelationCharge.R R/411-extractDrugBCUT.R R/415-extractDrugCPSA.R R/416-extractDrugCarbonTypes.R R/417-extractDrugChiChain.R R/424-extractDrugGravitationalIndex.R R/427-extractDrugHybridizationRatio.R R/428-extractDrugIPMolecularLearning.R R/429-extractDrugKappaShapeIndices.R R/430-extractDrugKierHallSmarts.R R/436-extractDrugMannholdLogP.R R/445-extractDrugWHIM.R R/471-extractDrugStandard.R R/472-extractDrugExtended.R R/473-extractDrugGraph.R R/474-extractDrugHybridization.R R/475-extractDrugMACCS.R R/476-extractDrugEstate.R R/477-extractDrugPubChem.R R/478-extractDrugKR.R R/479-extractDrugShortestPath.R R/480-extractDrugOBFP2.R R/481-extractDrugOBFP3.R R/482-extractDrugOBFP4.R R/485-extractDrugAP.R R/501-extractProtAAC.R R/502-extractProtDC.R R/503-extractProtTC.R R/504-extractProtMoreauBroto.R R/505-extractProtMoran.R R/506-extractProtGeary.R R/507-extractProtCTDC.R R/507-extractProtCTDCClass.R R/508-extractProtCTDT.R R/508-extractProtCTDTClass.R R/509-extractProtCTDD.R R/509-extractProtCTDDClass.R R/510-extractProtCTriad.R R/510-extractProtCTriadClass.R R/511-extractProtSOCN.R R/512-extractProtQSO.R R/513-extractProtPAAC.R R/514-extractProtAPAAC.R R/515-extractPCMScales.R R/515-extractPCMScalesGap.R R/516-extractPCMDescScales.R R/517-extractPCMPropScales.R R/517-extractPCMPropScalesGap.R R/518-extractPCMFAScales.R R/519-extractPCMMDSScales.R R/520-extractPCMBLOSUM.R R/521-extractProtPSSM.R R/522-extractProtPSSMFeature.R R/523-extractProtPSSMAcc.R R/600-make_kmer_index.R R/601-extractDNAkmer.R R/602-extractDNAIncDiv.R R/603-extractDNADAC.R R/604-extractDNADCC.R R/605-extractDNADACC.R R/606-extractDNATAC.R R/607-extractDNATCC.R R/608-extractDNATACC.R R/609-extractDNAPseDNC.R R/610-extractDNAPseKNC.R R/701-readFASTA.R R/702-readPDB.R R/703-readMolFromSDF.R R/704-readMolFromSmi.R R/705-searchDrug.R R/706-checkProt.R R/707-checkDNA.R R/708-revchars.R R/709-convMolFormat.R R/710-segProt.R R/711-acc.R R/712-plotStructure.R R/713-convSDFtoAP.R R/714-convAPtoFP.R R/801-getCPI.R R/901-calcDrugFPSim.R R/903-calcProtGOSim.R R/904-calcProtSeqSim.R R/906-parSeqSim.R R/907-parGOSim.R R/BioMedR-datalist.R README.MD inst/doc/BioMedR.pdf inst/examples/BioMedR-package-ex.R inst/unitTests/test_acc.R inst/unitTests/test_checkProt.R inst/unitTests/test_extractPCMBLOSUM.R inst/unitTests/test_extractProtAAC.R inst/unitTests/test_getCPI.R inst/unitTests/test_getPPI.R man/AA2DACOR.Rd man/AA3DMoRSE.Rd man/AAACF.Rd man/AABLOSUM100.Rd man/AABLOSUM45.Rd man/AABLOSUM50.Rd man/AABLOSUM62.Rd man/AABLOSUM80.Rd man/AABurden.Rd man/AACPSA.Rd man/AAConn.Rd man/AAConst.Rd man/AADescAll.Rd man/AAEdgeAdj.Rd man/AAEigIdx.Rd man/AAFGC.Rd man/AAGETAWAY.Rd man/AAGeom.Rd man/AAInfo.Rd man/AAMOE2D.Rd man/AAMOE3D.Rd man/AAMetaInfo.Rd man/AAMolProp.Rd man/AAPAM120.Rd man/AAPAM250.Rd man/AAPAM30.Rd man/AAPAM40.Rd man/AAPAM70.Rd man/AARDF.Rd man/AARandic.Rd man/AATopo.Rd man/AATopoChg.Rd man/AAWHIM.Rd man/AAWalk.Rd man/AAindex.Rd man/Autocorrelation.Rd man/BMgetDNAGenBank.Rd man/BioMedR-package.Rd man/Constitutional.Rd man/NNeighbors.Rd man/OptAA3d.Rd man/acc.Rd man/apfp.Rd man/atomprop.Rd man/bcl.Rd man/calcDrugFPSim.Rd man/calcParProtGOSim.Rd man/calcParProtSeqSim.Rd man/calcTwoProtGOSim.Rd man/calcTwoProtSeqSim.Rd man/checkDNA.Rd man/checkProt.Rd man/clusterCMP.Rd man/clusterJP.Rd man/clusterMDS.Rd man/clusterPlotSOMmap.Rd man/clusterStat.Rd man/connectivity.Rd man/convAPtoFP.Rd man/convMolFormat.Rd man/convSDFtoAP.Rd man/diversity.Rd man/extrDNADAC.Rd man/extrDNADACC.Rd man/extrDNADCC.Rd man/extrDNAIncDiv.Rd man/extrDNAPseDNC.Rd man/extrDNAPseKNC.Rd man/extrDNATAC.Rd man/extrDNATACC.Rd man/extrDNATCC.Rd man/extrDNAkmer.Rd man/extrDrugAIO.Rd man/extrDrugAP.Rd man/extrDrugBCUT.Rd man/extrDrugCPSA.Rd man/extrDrugEstate.Rd man/extrDrugEstateComplete.Rd man/extrDrugExtended.Rd man/extrDrugExtendedComplete.Rd man/extrDrugGraph.Rd man/extrDrugGraphComplete.Rd man/extrDrugHybridization.Rd man/extrDrugHybridizationComplete.Rd man/extrDrugHybridizationRatio.Rd man/extrDrugIPMolecularLearning.Rd man/extrDrugKR.Rd man/extrDrugKRComplete.Rd man/extrDrugKappaShapeIndices.Rd man/extrDrugKierHallSmarts.Rd man/extrDrugMACCS.Rd man/extrDrugMACCSComplete.Rd man/extrDrugMannholdLogP.Rd man/extrDrugOBFP2.Rd man/extrDrugOBFP3.Rd man/extrDrugOBFP4.Rd man/extrDrugPubChem.Rd man/extrDrugPubChemComplete.Rd man/extrDrugShortestPath.Rd man/extrDrugShortestPathComplete.Rd man/extrDrugStandard.Rd man/extrDrugStandardComplete.Rd man/extrDrugWHIM.Rd man/extrPCMBLOSUM.Rd man/extrPCMDescScales.Rd man/extrPCMFAScales.Rd man/extrPCMMDSScales.Rd man/extrPCMPropScales.Rd man/extrPCMScaleGap.Rd man/extrPCMScales.Rd man/extrProtAAC.Rd man/extrProtAPAAC.Rd man/extrProtCTDC.Rd man/extrProtCTDCClass.Rd man/extrProtCTDD.Rd man/extrProtCTDDClass.Rd man/extrProtCTDT.Rd man/extrProtCTDTClass.Rd man/extrProtCTriad.Rd man/extrProtCTriadClass.Rd man/extrProtDC.Rd man/extrProtFPGap.Rd man/extrProtGeary.Rd man/extrProtMoran.Rd man/extrProtMoreauBroto.Rd man/extrProtPAAC.Rd man/extrProtPSSM.Rd man/extrProtPSSMAcc.Rd man/extrProtPSSMFeature.Rd man/extrProtQSO.Rd man/extrProtSOCN.Rd man/extrProtTC.Rd man/geometric.Rd man/getCPI.Rd man/getDrug.Rd man/getProt.Rd man/id_x_s.Rd man/make_kmer_index.Rd man/parGOSim.Rd man/parSeqSim.Rd man/plotStructure.Rd man/pls.cv.Rd man/property.Rd man/readFASTA.Rd man/readMolFromSDF.Rd man/readMolFromSmi.Rd man/readPDB.Rd man/revchars.Rd man/rf.cv.Rd man/rf.fs.Rd man/sdfbcl.Rd man/searchDrug.Rd man/segProt.Rd man/som.bcl.Rd man/topology.Rd man/twoGOSim.Rd man/twoSeqSim.Rd tests/runTests.R vignettes/fig/CTD.pdf vignettes/fig/ctriad.pdf vignettes/fig/ex1-1.pdf vignettes/fig/ex1-2.pdf vignettes/fig/ex2-1.pdf vignettes/fig/ex3-1.pdf vignettes/fig/ex4-1.pdf vignettes/fig/ex4-2.pdf vignettes/fig/ex5-1.pdf vignettes/fig/ex6-1.pdf vignettes/fig/ex7-2.pdf vignettes/fig/logo-panel-text.pdf vignettes/fig/mds.pdf vignettes/fig/somplot.pdf