Man pages for wind22zhu/BioMedR
Generating Various Molecular Representations for Chemicals, Proteins, DNAs/RNAs and Their Interactions

AA2DACOR2D Autocorrelations Descriptors for 20 Amino Acids calculated...
AA3DMoRSE3D-MoRSE Descriptors for 20 Amino Acids calculated by Dragon
AAACFAtom-Centred Fragments Descriptors for 20 Amino Acids...
AABLOSUM100BLOSUM100 Matrix for 20 Amino Acids
AABLOSUM45BLOSUM45 Matrix for 20 Amino Acids
AABLOSUM50BLOSUM50 Matrix for 20 Amino Acids
AABLOSUM62BLOSUM62 Matrix for 20 Amino Acids
AABLOSUM80BLOSUM80 Matrix for 20 Amino Acids
AABurdenBurden Eigenvalues Descriptors for 20 Amino Acids calculated...
AAConnConnectivity Indices Descriptors for 20 Amino Acids...
AAConstConstitutional Descriptors for 20 Amino Acids calculated by...
AACPSACPSA Descriptors for 20 Amino Acids calculated by Discovery...
AADescAllAll 2D Descriptors for 20 Amino Acids calculated by Dragon
AAEdgeAdjEdge Adjacency Indices Descriptors for 20 Amino Acids...
AAEigIdxEigenvalue-Based Indices Descriptors for 20 Amino Acids...
AAFGCFunctional Group Counts Descriptors for 20 Amino Acids...
AAGeomGeometrical Descriptors for 20 Amino Acids calculated by...
AAGETAWAYGETAWAY Descriptors for 20 Amino Acids calculated by Dragon
AAindexAAindex Data of 544 Physicochemical and Biological Properties...
AAInfoInformation Indices Descriptors for 20 Amino Acids calculated...
AAMetaInfoMeta Information for the 20 Amino Acids
AAMOE2D2D Descriptors for 20 Amino Acids calculated by MOE 2011.10
AAMOE3D3D Descriptors for 20 Amino Acids calculated by MOE 2011.10
AAMolPropMolecular Properties Descriptors for 20 Amino Acids...
AAPAM120PAM120 Matrix for 20 Amino Acids
AAPAM250PAM250 Matrix for 20 Amino Acids
AAPAM30PAM30 Matrix for 20 Amino Acids
AAPAM40PAM40 Matrix for 20 Amino Acids
AAPAM70PAM70 Matrix for 20 Amino Acids
AARandicRandic Molecular Profiles Descriptors for 20 Amino Acids...
AARDFRDF Descriptors for 20 Amino Acids calculated by Dragon
AATopoTopological Descriptors for 20 Amino Acids calculated by...
AATopoChgTopological Charge Indices Descriptors for 20 Amino Acids...
AAWalkWalk and Path Counts Descriptors for 20 Amino Acids...
AAWHIMWHIM Descriptors for 20 Amino Acids calculated by Dragon
accAuto Cross Covariance (ACC) for Generating Scales-Based...
apfpFrequent Atom Pairs
atompropStandard atomic weights
AutocorrelationCalculates the Moreau-Broto Autocorrelation Descriptors using...
bcl2D descriptors of bcl2
BioMedR-packageToolkit for Compound-Protein Interaction in Drug Discovery
BMgetDNAGenBankGet DNA/RNA Sequences from Genbank by GI ID
calcDrugFPSimCalculate Drug Molecule Similarity Derived by Molecular...
calcDrugMCSSimCalculate Drug Molecule Similarity Derived by Maximum Common...
calcParProtGOSimProtein Sequence Similarity Calculation based on Gene...
calcParProtSeqSimParallellized Protein Sequence Similarity Calculation based...
calcTwoProtGOSimProtein Similarity Calculation based on Gene Ontology (GO)...
calcTwoProtSeqSimProtein Sequence Alignment for Two Protein Sequences
checkDNACheck if the DNA sequence are in the 4 default types
checkProtCheck if the protein sequence's amino acid types are the 20...
clusterCMPcluster compounds using a descriptor database
clusterJPJarvis-Patrick Clustering
clusterMDSvisualize clustering result using multi-dimensional scaling
clusterStatgenerate statistics on sizes of clusters
connectivityCalculate the Kier and Hall Chi Chain Indices of Orders 3, 4,...
ConstitutionalCalculates the Number of Amino Acids Descriptor
convAPtoFPFingerprints from descriptor vectors
convSDFtoAPAtom pair library
diversitydiversity function for make_kmer_vec
extrDNADACThe Dinucleotide-based Auto Covariance Descriptor
extrDNADACCThe Dinucleotide-based Auto-cross Covariance Descriptor
extrDNADCCThe Dinucleotide-based Cross Covariance Descriptor
extrDNAIncDivThe Increment Of Diversity Descriptors
extrDNAkmerThe Basic Kmer Descriptor
extrDNAPseDNCThe Pseudo Dinucleotide Composition Descriptor
extrDNAPseKNCThe Pseudo K-tupler Composition Descriptor
extrDNATACThe Trinucleotide-based Auto Covariance Descriptor
extrDNATACCThe Trinucleotide-based Auto-cross Covariance Descriptor
extrDNATCCThe Trinucleotide-based Cross Covariance Descriptor
extrDrugAIOCalculates All the Molecular Descriptors in the BioMedR...
extrDrugAPCalculate the Atom Pair Fingerprints
extrDrugBCUTBCUT - Eigenvalue Based Descriptor
extrDrugCPSAA Variety of Descriptors Combining Surface Area and Partial...
extrDrugEstateCalculate the E-State Molecular Fingerprints (in Compact...
extrDrugEstateCompleteCalculate the E-State Molecular Fingerprints (in Complete...
extrDrugExtendedCalculate the Extended Molecular Fingerprints (in Compact...
extrDrugExtendedCompleteCalculate the Extended Molecular Fingerprints (in Complete...
extrDrugGraphCalculate the Graph Molecular Fingerprints (in Compact...
extrDrugGraphCompleteCalculate the Graph Molecular Fingerprints (in Complete...
extrDrugHybridizationCalculate the Hybridization Molecular Fingerprints (in...
extrDrugHybridizationCompleteCalculate the Hybridization Molecular Fingerprints (in...
extrDrugHybridizationRatioDescriptor that Characterizing Molecular Complexity in Terms...
extrDrugIPMolecularLearningCalculates the Descriptor that Evaluates the Ionization...
extrDrugKappaShapeIndicesDescriptor that Calculates Kier and Hall Kappa Molecular...
extrDrugKierHallSmartsDescriptor that Counts the Number of Occurrences of the...
extrDrugKRCalculate the KR (Klekota and Roth) Molecular Fingerprints...
extrDrugKRCompleteCalculate the KR (Klekota and Roth) Molecular Fingerprints...
extrDrugMACCSCalculate the MACCS Molecular Fingerprints (in Compact...
extrDrugMACCSCompleteCalculate the MACCS Molecular Fingerprints (in Complete...
extrDrugMannholdLogPDescriptor that Calculates the LogP Based on a Simple...
extrDrugOBFP2Calculate the FP2 Molecular Fingerprints
extrDrugOBFP3Calculate the FP3 Molecular Fingerprints
extrDrugOBFP4Calculate the FP4 Molecular Fingerprints
extrDrugPubChemCalculate the PubChem Molecular Fingerprints (in Compact...
extrDrugPubChemCompleteCalculate the PubChem Molecular Fingerprints (in Complete...
extrDrugShortestPathCalculate the Shortest Path Molecular Fingerprints (in...
extrDrugShortestPathCompleteCalculate the Shortest Path Molecular Fingerprints (in...
extrDrugStandardCalculate the Standard Molecular Fingerprints (in Compact...
extrDrugStandardCompleteCalculate the Standard Molecular Fingerprints (in Complete...
extrDrugWHIMCalculate Holistic Descriptors Described by Todeschini et al.
extrPCMBLOSUMGeneralized BLOSUM and PAM Matrix-Derived Descriptors
extrPCMDescScalesScales-Based Descriptors with 20+ classes of Molecular...
extrPCMFAScalesGeneralized Scales-Based Descriptors derived by Factor...
extrPCMMDSScalesGeneralized Scales-Based Descriptors derived by...
extrPCMPropScalesGeneralized AA-Properties Based Scales Descriptors
extrPCMScaleGapScales-Based Descriptors derived by Principal Components...
extrPCMScalesGeneralized Scales-Based Descriptors derived by Principal...
extrProtAACAmino Acid Composition Descriptor
extrProtAPAACAmphiphilic Pseudo Amino Acid Composition Descriptor
extrProtCTDCCTD Descriptors - Composition
extrProtCTDCClassCTD Descriptors - Composition (with Customized Amino Acid...
extrProtCTDDCTD Descriptors - Distribution
extrProtCTDDClassCTD Descriptors - Distribution (with Customized Amino Acid...
extrProtCTDTCTD Descriptors - Transition
extrProtCTDTClassCTD Descriptors - Transition (with Customized Amino Acid...
extrProtCTriadConjoint Triad Descriptor
extrProtCTriadClassConjoint Triad Descriptor (with Customized Amino Acid...
extrProtDCDipeptide Composition Descriptor
extrProtFPGapAmino Acid Properties Based Scales Descriptors (Protein...
extrProtGearyGeary Autocorrelation Descriptor
extrProtMoranMoran Autocorrelation Descriptor
extrProtMoreauBrotoNormalized Moreau-Broto Autocorrelation Descriptor
extrProtPAACPseudo Amino Acid Composition Descriptor
extrProtPSSMCompute PSSM (Position-Specific Scoring Matrix) for given...
extrProtPSSMAccProfile-based protein representation derived by PSSM...
extrProtPSSMFeatureProfile-based protein representation derived by PSSM...
extrProtQSOQuasi-Sequence-Order (QSO) Descriptor
extrProtSOCNSequence-Order-Coupling Numbers
extrProtTCTripeptide Composition Descriptor
geometricDescriptor Characterizing the Mass Distribution of the...
getCPIGenerating Interaction Descriptors
getDrugRetrieve Drug Molecules in MOL and SMILES Format from...
getProtRetrieve Protein Sequence in various Formats from Databases
id_x_sid_x_s function for make_kmer_vec
make_kmer_indexCalculate The Basic Kmer Feature Vector
NNeighborsNearest Neighbors
OptAA3dOptAA3d.sdf - 20 Amino Acids Optimized with MOE 2011.10...
parGOSimProtein/DNA Sequence Similarity Calculation based on Gene...
parSeqSimParallellized Protein/DVA Sequence Similarity Calculation...
plotStructurePlots compound structure(s) for molecules stored in SDF and...
pls.cvThe Cross-Validation of Classification and Regression models...
propertyCalculates Atom Additive logP and Molar Refractivity Values...
readFASTARead Protein/DNA Sequences in FASTA Format
readMolFromSDFRead Molecules from SDF Files and Return Parsed Java...
readMolFromSmiRead Molecules from SMILES Files and Return Parsed Java...
readPDBRead Protein Sequences in PDB Format
revcharsThe Reverse chars
rf.cvThe Cross-Validation of Classification and Regression models...
rf.fsRandom Forest Cross-Valdidation for feature selection
sdfbclSD file in 'SDFset' object
searchDrugParallelized Drug Molecule Similarity Search by Molecular...
segProtProtein Sequence Segmentation
topologyTopological Descriptor Characterizing the Carbon Connectivity...
twoGOSimProtein/DNA Similarity Calculation based on Gene Ontology...
twoSeqSimProtein/DNA Sequence Alignment for Two Protein Sequences
wind22zhu/BioMedR documentation built on April 18, 2018, 1:28 a.m.