| AA2DACOR | 2D Autocorrelations Descriptors for 20 Amino Acids calculated... |
| AA3DMoRSE | 3D-MoRSE Descriptors for 20 Amino Acids calculated by Dragon |
| AAACF | Atom-Centred Fragments Descriptors for 20 Amino Acids... |
| AABLOSUM100 | BLOSUM100 Matrix for 20 Amino Acids |
| AABLOSUM45 | BLOSUM45 Matrix for 20 Amino Acids |
| AABLOSUM50 | BLOSUM50 Matrix for 20 Amino Acids |
| AABLOSUM62 | BLOSUM62 Matrix for 20 Amino Acids |
| AABLOSUM80 | BLOSUM80 Matrix for 20 Amino Acids |
| AABurden | Burden Eigenvalues Descriptors for 20 Amino Acids calculated... |
| AAConn | Connectivity Indices Descriptors for 20 Amino Acids... |
| AAConst | Constitutional Descriptors for 20 Amino Acids calculated by... |
| AACPSA | CPSA Descriptors for 20 Amino Acids calculated by Discovery... |
| AADescAll | All 2D Descriptors for 20 Amino Acids calculated by Dragon |
| AAEdgeAdj | Edge Adjacency Indices Descriptors for 20 Amino Acids... |
| AAEigIdx | Eigenvalue-Based Indices Descriptors for 20 Amino Acids... |
| AAFGC | Functional Group Counts Descriptors for 20 Amino Acids... |
| AAGeom | Geometrical Descriptors for 20 Amino Acids calculated by... |
| AAGETAWAY | GETAWAY Descriptors for 20 Amino Acids calculated by Dragon |
| AAindex | AAindex Data of 544 Physicochemical and Biological Properties... |
| AAInfo | Information Indices Descriptors for 20 Amino Acids calculated... |
| AAMetaInfo | Meta Information for the 20 Amino Acids |
| AAMOE2D | 2D Descriptors for 20 Amino Acids calculated by MOE 2011.10 |
| AAMOE3D | 3D Descriptors for 20 Amino Acids calculated by MOE 2011.10 |
| AAMolProp | Molecular Properties Descriptors for 20 Amino Acids... |
| AAPAM120 | PAM120 Matrix for 20 Amino Acids |
| AAPAM250 | PAM250 Matrix for 20 Amino Acids |
| AAPAM30 | PAM30 Matrix for 20 Amino Acids |
| AAPAM40 | PAM40 Matrix for 20 Amino Acids |
| AAPAM70 | PAM70 Matrix for 20 Amino Acids |
| AARandic | Randic Molecular Profiles Descriptors for 20 Amino Acids... |
| AARDF | RDF Descriptors for 20 Amino Acids calculated by Dragon |
| AATopo | Topological Descriptors for 20 Amino Acids calculated by... |
| AATopoChg | Topological Charge Indices Descriptors for 20 Amino Acids... |
| AAWalk | Walk and Path Counts Descriptors for 20 Amino Acids... |
| AAWHIM | WHIM Descriptors for 20 Amino Acids calculated by Dragon |
| acc | Auto Cross Covariance (ACC) for Generating Scales-Based... |
| apfp | Frequent Atom Pairs |
| atomprop | Standard atomic weights |
| Autocorrelation | Calculates the Moreau-Broto Autocorrelation Descriptors using... |
| bcl | 2D descriptors of bcl2 |
| BioMedR-package | Toolkit for Compound-Protein Interaction in Drug Discovery |
| BMgetDNAGenBank | Get DNA/RNA Sequences from Genbank by GI ID |
| calcDrugFPSim | Calculate Drug Molecule Similarity Derived by Molecular... |
| calcParProtGOSim | Protein Sequence Similarity Calculation based on Gene... |
| calcParProtSeqSim | Parallellized Protein Sequence Similarity Calculation based... |
| calcTwoProtGOSim | Protein Similarity Calculation based on Gene Ontology (GO)... |
| calcTwoProtSeqSim | Protein Sequence Alignment for Two Protein Sequences |
| checkDNA | Check if the DNA sequence are in the 4 default types |
| checkProt | Check if the protein sequence's amino acid types are the 20... |
| clusterCMP | cluster compounds using a descriptor database |
| clusterJP | Jarvis-Patrick Clustering |
| clusterMDS | visualize clustering result using multi-dimensional scaling |
| clusterPlotSOMmap | Plot self-organising map |
| clusterStat | generate statistics on sizes of clusters |
| connectivity | Calculate the Kier and Hall Chi Chain Indices of Orders 3, 4,... |
| Constitutional | Calculates the Number of Amino Acids Descriptor |
| convAPtoFP | Fingerprints from descriptor vectors |
| convSDFtoAP | Atom pair library |
| diversity | diversity function for make_kmer_vec |
| extrDNADAC | The Dinucleotide-based Auto Covariance Descriptor |
| extrDNADACC | The Dinucleotide-based Auto-cross Covariance Descriptor |
| extrDNADCC | The Dinucleotide-based Cross Covariance Descriptor |
| extrDNAIncDiv | The Increment Of Diversity Descriptors |
| extrDNAkmer | The Basic Kmer Descriptor |
| extrDNAPseDNC | The Pseudo Dinucleotide Composition Descriptor |
| extrDNAPseKNC | The Pseudo K-tupler Composition Descriptor |
| extrDNATAC | The Trinucleotide-based Auto Covariance Descriptor |
| extrDNATACC | The Trinucleotide-based Auto-cross Covariance Descriptor |
| extrDNATCC | The Trinucleotide-based Cross Covariance Descriptor |
| extrDrugAIO | Calculates All the Molecular Descriptors in the BioMedR... |
| extrDrugAP | Calculate the Atom Pair Fingerprints |
| extrDrugBCUT | BCUT - Eigenvalue Based Descriptor |
| extrDrugCPSA | A Variety of Descriptors Combining Surface Area and Partial... |
| extrDrugEstate | Calculate the E-State Molecular Fingerprints (in Compact... |
| extrDrugEstateComplete | Calculate the E-State Molecular Fingerprints (in Complete... |
| extrDrugExtended | Calculate the Extended Molecular Fingerprints (in Compact... |
| extrDrugExtendedComplete | Calculate the Extended Molecular Fingerprints (in Complete... |
| extrDrugGraph | Calculate the Graph Molecular Fingerprints (in Compact... |
| extrDrugGraphComplete | Calculate the Graph Molecular Fingerprints (in Complete... |
| extrDrugHybridization | Calculate the Hybridization Molecular Fingerprints (in... |
| extrDrugHybridizationComplete | Calculate the Hybridization Molecular Fingerprints (in... |
| extrDrugHybridizationRatio | Descriptor that Characterizing Molecular Complexity in Terms... |
| extrDrugIPMolecularLearning | Calculates the Descriptor that Evaluates the Ionization... |
| extrDrugKappaShapeIndices | Descriptor that Calculates Kier and Hall Kappa Molecular... |
| extrDrugKierHallSmarts | Descriptor that Counts the Number of Occurrences of the... |
| extrDrugKR | Calculate the KR (Klekota and Roth) Molecular Fingerprints... |
| extrDrugKRComplete | Calculate the KR (Klekota and Roth) Molecular Fingerprints... |
| extrDrugMACCS | Calculate the MACCS Molecular Fingerprints (in Compact... |
| extrDrugMACCSComplete | Calculate the MACCS Molecular Fingerprints (in Complete... |
| extrDrugMannholdLogP | Descriptor that Calculates the LogP Based on a Simple... |
| extrDrugPubChem | Calculate the PubChem Molecular Fingerprints (in Compact... |
| extrDrugPubChemComplete | Calculate the PubChem Molecular Fingerprints (in Complete... |
| extrDrugShortestPath | Calculate the Shortest Path Molecular Fingerprints (in... |
| extrDrugShortestPathComplete | Calculate the Shortest Path Molecular Fingerprints (in... |
| extrDrugStandard | Calculate the Standard Molecular Fingerprints (in Compact... |
| extrDrugStandardComplete | Calculate the Standard Molecular Fingerprints (in Complete... |
| extrDrugWHIM | Calculate Holistic Descriptors Described by Todeschini et al. |
| extrPCMBLOSUM | Generalized BLOSUM and PAM Matrix-Derived Descriptors |
| extrPCMDescScales | Scales-Based Descriptors with 20+ classes of Molecular... |
| extrPCMFAScales | Generalized Scales-Based Descriptors derived by Factor... |
| extrPCMMDSScales | Generalized Scales-Based Descriptors derived by... |
| extrPCMPropScales | Generalized AA-Properties Based Scales Descriptors |
| extrPCMScaleGap | Scales-Based Descriptors derived by Principal Components... |
| extrPCMScales | Generalized Scales-Based Descriptors derived by Principal... |
| extrProtAAC | Amino Acid Composition Descriptor |
| extrProtAPAAC | Amphiphilic Pseudo Amino Acid Composition Descriptor |
| extrProtCTDC | CTD Descriptors - Composition |
| extrProtCTDCClass | CTD Descriptors - Composition (with Customized Amino Acid... |
| extrProtCTDD | CTD Descriptors - Distribution |
| extrProtCTDDClass | CTD Descriptors - Distribution (with Customized Amino Acid... |
| extrProtCTDT | CTD Descriptors - Transition |
| extrProtCTDTClass | CTD Descriptors - Transition (with Customized Amino Acid... |
| extrProtCTriad | Conjoint Triad Descriptor |
| extrProtCTriadClass | Conjoint Triad Descriptor (with Customized Amino Acid... |
| extrProtDC | Dipeptide Composition Descriptor |
| extrProtFPGap | Amino Acid Properties Based Scales Descriptors (Protein... |
| extrProtGeary | Geary Autocorrelation Descriptor |
| extrProtMoran | Moran Autocorrelation Descriptor |
| extrProtMoreauBroto | Normalized Moreau-Broto Autocorrelation Descriptor |
| extrProtPAAC | Pseudo Amino Acid Composition Descriptor |
| extrProtPSSM | Compute PSSM (Position-Specific Scoring Matrix) for given... |
| extrProtPSSMAcc | Profile-based protein representation derived by PSSM... |
| extrProtPSSMFeature | Profile-based protein representation derived by PSSM... |
| extrProtQSO | Quasi-Sequence-Order (QSO) Descriptor |
| extrProtSOCN | Sequence-Order-Coupling Numbers |
| extrProtTC | Tripeptide Composition Descriptor |
| geometric | Descriptor Characterizing the Mass Distribution of the... |
| getCPI | Generating Interaction Descriptors |
| getDrug | Retrieve Drug Molecules in MOL and SMILES Format from... |
| getProt | Retrieve Protein Sequence in various Formats from Databases |
| id_x_s | id_x_s function for make_kmer_vec |
| make_kmer_index | Calculate The Basic Kmer Feature Vector |
| NNeighbors | Nearest Neighbors |
| OptAA3d | OptAA3d.sdf - 20 Amino Acids Optimized with MOE 2011.10... |
| parGOSim | Protein/DNA Sequence Similarity Calculation based on Gene... |
| parSeqSim | Parallellized Protein/DVA Sequence Similarity Calculation... |
| plotStructure | Plots compound structure(s) for molecules stored in SDF and... |
| pls.cv | The Cross-Validation of Classification and Regression models... |
| property | Calculates Atom Additive logP and Molar Refractivity Values... |
| readFASTA | Read Protein/DNA Sequences in FASTA Format |
| readMolFromSDF | Read Molecules from SDF Files and Return Parsed Java... |
| readMolFromSmi | Read Molecules from SMILES Files and Return Parsed Java... |
| readPDB | Read Protein Sequences in PDB Format |
| revchars | The Reverse chars |
| rf.cv | The Cross-Validation of Classification and Regression models... |
| rf.fs | Random Forest Cross-Valdidation for feature selection |
| sdfbcl | SD file in 'SDFset' object |
| searchDrug | Parallelized Drug Molecule Similarity Search by Molecular... |
| segProt | Protein Sequence Segmentation |
| som.bcl | kohonen object |
| topology | Topological Descriptor Characterizing the Carbon Connectivity... |
| twoGOSim | Protein/DNA Similarity Calculation based on Gene Ontology... |
| twoSeqSim | Protein/DNA Sequence Alignment for Two Protein Sequences |
