Feature Extraction from Biological Sequences
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Documentation for package ‘ftrCOOL’ version 2.0.0
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A B C D E F G K L M N O P Q R S T Z
-- A --
| AA2Binary | Amino Acid To Binary (AA2Binary) |
| AAindex | Amino Acid Index (AAindex) |
| AAKpartComposition | Amino Acid to K Part Composition (AAKpartComposition) |
| AAutoCor | Amino Acid Autocorrelation-Autocovariance (AAutoCor) |
| AESNN3 | Learn from alignments (AESNN3) |
| alphabetCheck | AlphabetCheck |
| ANF_DNA | Accumulated Nucleotide Frequency (ANF_DNA) |
| ANF_RNA | Accumulated riboNucleotide Frequency (ANF_RNA) |
| APAAC | Amphiphilic Pseudo-Amino Acid Composition(series) (APAAC) |
| APkNUCdi_DNA | Amphiphilic Pseudo-k Nucleotide Composition-di(series) (APkNUCdi_DNA) |
| APkNUCdi_RNA | Amphiphilic Pseudo-k riboNucleotide Composition-di(series) (APkNUCdi_RNA) |
| APkNUCTri_DNA | Amphiphilic Pseudo-k Nucleotide Composition-Tri(series) (APkNUCTri_DNA) |
| ASA | Accessible Solvent Accessibility (ASA) |
| ASDC | Adaptive skip dipeptide composition (ASDC) |
| ASDC_DNA | Adaptive skip dinucleotide composition_DNA) (ASDC_DNA) |
| ASDC_RNA | Adaptive skip di-ribonucleotide composition) (ASDC_RNA) |
| AutoCorDiNUC_DNA | Di Nucleotide Autocorrelation-Autocovariance (AutoCorDiNUC_DNA) |
| AutoCorDiNUC_RNA | Di riboNucleotide Autocorrelation-Autocovariance (AutoCorDiNUC_RNA) |
| AutoCorTriNUC_DNA | Tri Nucleotide Autocorrelation-Autocovariance (AutoCorTriNUC_DNA) |
-- B --
| binary_3bit_T1 | Binary - 3bit - Type1 (binary_3bit_T1) |
| binary_3bit_T2 | Binary - 3bit - Type2 (binary_3bit_T2) |
| binary_3bit_T3 | Binary - 3bit - Type3 (binary_3bit_T3) |
| binary_3bit_T4 | Binary - 3bit - Type4 (binary_3bit_T4) |
| binary_3bit_T5 | Binary - 3bit - Type5 (binary_3bit_T5) |
| binary_3bit_T6 | Binary - 3bit - Type6 (binary_3bit_T6) |
| binary_3bit_T7 | Binary - 3bit - Type7 (binary_3bit_T7) |
| binary_5bit_T1 | Binary - 5bit - Type1 (binary_5bit_T1) |
| binary_5bit_T2 | Binary - 5bit - Type2 (binary_5bit_T2) |
| binary_6bit | Binary - 6bit (binary_6bit) |
| BLOSUM62 | Blosum62 (BLOSUM62) |
-- C --
| CkSAApair | Composition of k-Spaced Amino Acids pairs (CkSAApair) |
| CkSGAApair | Composition of k-Spaced Grouped Amino Acids pairs (CkSGAApair) |
| CkSNUCpair_DNA | Composition of k-Spaced Nucleotides Pairs (CkSNUCpair_DNA) |
| CkSNUCpair_RNA | Composition of k-Spaced riboNucleotides Pairs (CkSNUCpair_RNA) |
| codonAdaptionIndex | Codon Adaption Index (codonAdaptionIndex) |
| CodonFraction | Codon Fraction (CodonFraction) |
| CodonUsage_DNA | Codon Usage in DNA (CodonUsage_DNA) |
| CodonUsage_RNA | Codon Usage in RNA (CodonUsage_RNA) |
| conjointTriad | Conjoint Triad (conjointTriad) |
| conjointTriadKS | k-Spaced Conjoint Triad (conjointTriadKS) |
| CTD | Composition_Transition_Distribution (CTD) |
| CTDC | CTD Composition (CTDC) |
| CTDD | CTD Distribution (CTDD) |
| CTDT | CTD Transition (CTDT) |
-- D --
| DDE | Dipeptide Deviation from Expected Mean value (DDE) |
| DiNUC2Binary_DNA | Dinucleotide To Binary DNA (DiNUC2Binary_DNA) |
| DiNUC2Binary_RNA | Di riboNucleotide To Binary RNA (DiNUC2Binary_RNA) |
| DiNUCindex_DNA | Di Nucleotide Index (DiNUCindex_DNA) |
| DiNUCindex_RNA | Di riboNucleotide Index (DiNUCindex_RNA) |
| DisorderB | disorder Binary (DisorderB) |
| DisorderC | disorder Content (DisorderC) |
| DisorderS | disorder Simple (DisorderS) |
| DistancePair | PseAAC of distance-pairs and reduced alphabet (DistancePair) |
| DPCP_DNA | Dinucleotide physicochemical properties (DPCP_DNA) |
| DPCP_RNA | Di-ribonucleotide physicochemical properties (DPCP_RNA) |
-- E --
| EAAComposition | Enhanced Amino Acid Composition (EAAComposition) |
| EffectiveNumberCodon | Effective Number of Codon (EffectiveNumberCodon) |
| EGAAComposition | Enhanced Grouped Amino Acid Composition (EGAAComposition) |
| EIIP | Electron-Ion Interaction Pseudopotentials (EIIP) |
| ENUComposition_DNA | Enhanced Nucleotide Composition (ENUComposition_DNA) |
| ENUComposition_RNA | Enhanced riboNucleotide Composition (ENUComposition_RNA) |
| ExpectedValKmerNUC_DNA | Expected Value for K-mer Nucleotide (ExpectedValKmerNUC_DNA) |
| ExpectedValKmerNUC_RNA | Expected Value for K-mer riboNucleotide (ExpectedValKmerNUC_RNA) |
| ExpectedValueAA | Expected Value for each Amino Acid (ExpectedValueAA) |
| ExpectedValueGAA | Expected Value for Grouped Amino Acid (ExpectedValueGAA) |
| ExpectedValueGKmerAA | Expected Value for Grouped K-mer Amino Acid(ExpectedValueGKmerAA) |
| ExpectedValueKmerAA | Expected Value for K-mer Amino Acid (ExpectedValueKmerAA) |
-- F --
| fa.read | Fasta File Reader (fa.read) |
| fickettScore | Fickett Score (fickettScore) |
-- G --
| GAAKpartComposition | Grouped Amino Acid K Part Composition (GAAKpartComposition) |
| GrpDDE | Group Dipeptide Deviation from Expected Mean (GrpDDE) |
| G_Ccontent_DNA | G_C content in DNA (G_Ccontent_DNA) |
| G_Ccontent_RNA | G_C content in RNA (G_Ccontent_RNA) |
-- K --
| kAAComposition | k Amino Acid Composition (kAAComposition) |
| kGAAComposition | k Grouped Amino Acid Composition (kGAAComposition) |
| KNNPeptide | K-Nearest Neighbor for Peptides (KNNPeptide) |
| KNNProtein | K-Nearest Neighbor for Protein (KNNProtein) |
| KNN_DNA | K-Nearest Neighbor_DNA (KNN_DNA) |
| KNN_RNA | K-Nearest Neighbor_RNA (KNN_RNA) |
| kNUComposition_DNA | k Nucleotide Composition (kNUComposition_DNA) |
| kNUComposition_RNA | k riboNucleotide Composition (kNUComposition_RNA) |
-- L --
| LocalPoSpKAAF | Local Position Specific k Amino Acids Frequency (LocalPoSpKAAF) |
| LocalPoSpKNUCF_DNA | Local Position Specific k Nucleotide Frequency (LocalPoSpKNUCF_DNA) |
| LocalPoSpKNUCF_RNA | Local Position Specific k riboNucleotide Frequency (LocalPoSpKNUCF_RNA) |
-- M --
| maxORF | Maximum Open Reading Frame in DNA (maxORF) |
| maxORFlength_DNA | Maximum Open Reading Frame length in DNA (maxORFlength_DNA) |
| maxORFlength_RNA | Maximum Open Reading Frame length in RNA (maxORFlength_RNA) |
| maxORF_RNA | Maximum Open Reading Frame in RNA (maxORF_RNA) |
| Mismatch_DNA | Mismatch_DNA (Mismatch_DNA) |
| Mismatch_RNA | Mismatch_RNA (Mismatch_RNA) |
| MMI_DNA | Multivariate Mutual Information_DNA (MMI_DNA) |
| MMI_RNA | Multivariate Mutual Information_RNA (MMI_RNA) |
-- N --
| nameKmer | naming Kmer (nameKmer) |
| NCP_DNA | Nucleotide Chemical Property (NCP_DNA) |
| NCP_RNA | riboNucleotide Chemical Property (NCP_RNA) |
| needleman | Needleman-Wunsch (needleman) |
| nonStandardSeq | nonStandard sequence (nonStandardSeq) |
| NUC2Binary_DNA | Nucleotide To Binary (NUC2Binary_DNA) |
| NUC2Binary_RNA | riboNucleotide To Binary (NUC2Binary_RNA) |
| NUCKpartComposition_DNA | Nucleotide to K Part Composition (NUCKpartComposition_DNA) |
| NUCKpartComposition_RNA | riboNucleotide to K Part Composition (NUCKpartComposition_RNA) |
-- O --
| OPF_10bit | Overlapping Property Features_10bit (OPF_10bit) |
| OPF_7bit_T1 | Overlapping property features_7bit_T1 (OPF_7bit_T1) |
| OPF_7bit_T2 | Overlapping property features_7bit_T2 (OPF_7bit_T2) |
| OPF_7bit_T3 | Overlapping property features_7bit_T3 (OPF_7bit_T3) |
-- P --
| PCPseDNC | Parallel Correlation Pseudo Dinucleotide Composition (PCPseDNC) |
| PS2_DNA | Position-specific of two nucleotide_DNA (PS2_DNA) |
| PS2_RNA | Position-specific of two nucleotide_RNA (PS2_RNA) |
| PS3_DNA | Position-specific of three nucleotide_DNA (PS3_DNA) |
| PS3_RNA | Position-specific of three ribonucleotide_RNA (PS3_RNA) |
| PS4_DNA | Position-specific of four nucleotide_DNA (PS4_DNA) |
| PS4_RNA | Position-specific of four ribonucleotide (PS4_RNA) |
| PSEAAC | Pseudo-Amino Acid Composition (Parallel) (PSEAAC) |
| PseEIIP | Pseudo Electron-Ion Interaction Pseudopotentials of Trinucleotide (PseEIIP) |
| PSEkNUCdi_DNA | Pseudo k Nucleotide Composition-Di(Parallel) (PSEkNUCdi_DNA) |
| PSEkNUCdi_RNA | Pseudo k riboNucleotide Composition-Di(Parallel) (PSEkNUCdi_RNA) |
| PSEkNUCTri_DNA | Pseudo k Nucleotide Composition-Tri(Parallel) (PSEkNUCTri_RNA) |
| PseKRAAC_T1 | Pseudo K_tuple Reduced Amino Acid Composition Type-1 (PseKRAAC_T1) |
| PseKRAAC_T10 | Pseudo K_tuple Reduced Amino Acid Composition Type-10 (PseKRAAC_T10) |
| PseKRAAC_T11 | Pseudo K_tuple Reduced Amino Acid Composition Type-11 (PseKRAAC_T11) |
| PseKRAAC_T12 | Pseudo K_tuple Reduced Amino Acid Composition Type-12 (PseKRAAC_T12) |
| PseKRAAC_T13 | Pseudo K_tuple Reduced Amino Acid Composition Type_13 (PseKRAAC_T13) |
| PseKRAAC_T14 | Pseudo K_tuple Reduced Amino Acid Composition Type-14 (PseKRAAC_T14) |
| PseKRAAC_T15 | Pseudo K_tuple Reduced Amino Acid Composition Type-15 (PseKRAAC_T15) |
| PseKRAAC_T16 | Pseudo K_tuple Reduced Amino Acid Composition Type-16 (PseKRAAC_T16) |
| PseKRAAC_T2 | Pseudo K_tuple Reduced Amino Acid Composition Type-2 (PseKRAAC_T2) |
| PseKRAAC_T3A | Pseudo K_tuple Reduced Amino Acid Composition Type-3A (PseKRAAC_T3A) |
| PseKRAAC_T3B | Pseudo K_tuple Reduced Amino Acid Composition Type_3B (PseKRAAC_T3B) |
| PseKRAAC_T4 | Pseudo K_tuple Reduced Amino Acid Composition Type-4 (PseKRAAC_T4) |
| PseKRAAC_T5 | Pseudo K_tuple Reduced Amino Acid Composition Type-5 (PseKRAAC_T5) |
| PseKRAAC_T6A | Pseudo K_tuple Reduced Amino Acid Composition Type-6A (PseKRAAC_T6A) |
| PseKRAAC_T6B | Pseudo K_tuple Reduced Amino Acid Composition Type-6B (PseKRAAC_T6B) |
| PseKRAAC_T7 | Pseudo K_tuple Reduced Amino Acid Composition Type-7 (PseKRAAC_T7) |
| PseKRAAC_T8 | Pseudo K_tuple Reduced Amino Acid Composition Type-8 (PseKRAAC_T8) |
| PseKRAAC_T9 | Pseudo K_tuple Reduced Amino Acid Composition Type-9 (PseKRAAC_T9) |
| PSSM | Position-Specific Scoring Matrix (PSSM) |
| PSTNPds | Position-Specific Trinucleotide Propensity based on double-strand (PSTNPds) |
| PSTNPss_DNA | Position-Specific Trinucleotide Propensity based on single-strand DNA (PSTNPss_DNA) |
| PSTNPss_RNA | Position-Specific Tri-ribonucleotide Propensity based on single-strand RNA (PSTNPss_RNA) |
-- Q --
| QSOrder | Quasi Sequence Order (QSOrder) |
-- R --
| readASAdir | Read Directory of Accessible Solvent accessibility predicted files (readASAdir) |
| readDisDir | Read disorder predicted Directory (readDisDir) |
| readPSSMdir | Read PSSM Directory (readPSSMdir) |
| readss2Dir | Read ss2 predicted Directory (readss2Dir) |
| readTorsionDir | Read Directory of Torsion predicted files (readTorsionDir) |
| revComp | reverseCompelement (revComp) |
-- S --
| SAAC | Splitted Amino Acid Composition (SAAC) |
| SGAAC | Splitted Group Amino Acid Composition (SGAAC) |
| SOCNumber | Sequence Order Coupling Number (SOCNumber) |
| SSEB | Secondary Structure Elements Binary (SSEB) |
| SSEC | Secondary Structure Elements Composition (SSEC) |
| SSES | Secondary Structure Elements Simple (SSES) |
-- T --
| TorsionAngle | Torsion Angle (TorsionAngle) |
| TPCP_DNA | Trinucleotide physicochemical properties (TPCP_DNA) |
| TriNUCindex_DNA | Tri Nucleotide Index (TriNucIndex) |
-- Z --
| Zcurve12bit_DNA | Z_curve_12bit_DNA (Zcurve12bit_DNA) |
| Zcurve12bit_RNA | Z_curve_12bit_RNA (Zcurve12bit_RNA) |
| Zcurve144bit_DNA | Z_curve_144bit_DNA (Zcurve144bit_DNA) |
| Zcurve144bit_RNA | Z_curve_144bit_RNA (Zcurve144bit_RNA) |
| Zcurve36bit_DNA | Z_curve_36bit_DNA (Zcurve36bit_DNA) |
| Zcurve36bit_RNA | Z_curve_36bit_RNA (Zcurve36bit_RNA) |
| Zcurve48bit_DNA | Z_curve_48bit_DNA (Zcurve48bit_DNA) |
| Zcurve48bit_RNA | Z_curve_48bit_RNA (Zcurve48bit_RNA) |
| Zcurve9bit_DNA | Z_curve_9bit_DNA (Zcurve9bit_DNA) |
| Zcurve9bit_RNA | Z_curve_9bit_RNA (Zcurve9bit_RNA) |
| zSCALE | Z-SCALE (zSCALE) |