Package: ftrCOOL 2.0.0

ftrCOOL: Feature Extraction from Biological Sequences

Extracts features from biological sequences. It contains most features which are presented in related work and also includes features which have never been introduced before. It extracts numerous features from nucleotide and peptide sequences. Each feature converts the input sequences to discrete numbers in order to use them as predictors in machine learning models. There are many features and information which are hidden inside a sequence. Utilizing the package, users can convert biological sequences to discrete models based on chosen properties. References: 'iLearn' 'Z. Chen et al.' (2019) <doi:10.1093/bib/bbz041>. 'iFeature' 'Z. Chen et al.' (2018) <doi:10.1093/bioinformatics/bty140>. <https://CRAN.R-project.org/package=rDNAse>. 'PseKRAAC' 'Y. Zuo et al.' 'PseKRAAC: a flexible web server for generating pseudo K-tuple reduced amino acids composition' (2017) <doi:10.1093/bioinformatics/btw564>. 'iDNA6mA-PseKNC' 'P. Feng et al.' 'iDNA6mA-PseKNC: Identifying DNA N6-methyladenosine sites by incorporating nucleotide physicochemical properties into PseKNC' (2019) <doi:10.1016/j.ygeno.2018.01.005>. 'I. Dubchak et al.' 'Prediction of protein folding class using global description of amino acid sequence' (1995) <doi:10.1073/pnas.92.19.8700>. 'W. Chen et al.' 'Identification and analysis of the N6-methyladenosine in the Saccharomyces cerevisiae transcriptome' (2015) <doi:10.1038/srep13859>.

Authors:Sare Amerifar

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ftrCOOL.pdf |ftrCOOL.html✨
ftrCOOL/json (API)
NEWS

# Install 'ftrCOOL' in R:
install.packages('ftrCOOL', repos = c('https://sareameri.r-universe.dev', 'https://cloud.r-project.org'))

Peer review:

On CRAN:

This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.

166 exports 1 stars 1.31 score 0 dependencies 3 dependents 1 mentions 1 scripts 337 downloads

Last updated 3 years agofrom:1bb6f0b92e. Checks:OK: 3 NOTE: 4. Indexed: yes.

TargetResultDate
Doc / VignettesOKSep 16 2024
R-4.5-winNOTESep 16 2024
R-4.5-linuxNOTESep 16 2024
R-4.4-winNOTESep 16 2024
R-4.4-macNOTESep 16 2024
R-4.3-winOKSep 16 2024
R-4.3-macOKSep 16 2024

Exports:AA2BinaryAAindexAAKpartCompositionAAutoCorAESNN3alphabetCheckANF_DNAANF_RNAAPAACAPkNUCdi_DNAAPkNUCdi_RNAAPkNUCTri_DNAASAASDCASDC_DNAASDC_RNAAutoCorDiNUC_DNAAutoCorDiNUC_RNAAutoCorTriNUC_DNAbinary_3bit_T1binary_3bit_T2binary_3bit_T3binary_3bit_T4binary_3bit_T5binary_3bit_T6binary_3bit_T7binary_5bit_T1binary_5bit_T2binary_6bitBLOSUM62CkSAApairCkSGAApairCkSNUCpair_DNACkSNUCpair_RNAcodonAdaptionIndexCodonFractionCodonUsage_DNACodonUsage_RNAconjointTriadconjointTriadKSCTDCTDCCTDDCTDTDDEDiNUC2Binary_DNADiNUC2Binary_RNADiNUCindex_DNADiNUCindex_RNADisorderBDisorderCDisorderSDistancePairDPCP_DNADPCP_RNAEAACompositionEffectiveNumberCodonEGAACompositionEIIPENUComposition_DNAENUComposition_RNAExpectedValKmerNUC_DNAExpectedValKmerNUC_RNAExpectedValueAAExpectedValueGAAExpectedValueGKmerAAExpectedValueKmerAAfa.readfickettScoreG_Ccontent_DNAG_Ccontent_RNAGAAKpartCompositionGrpDDEkAACompositionkGAACompositionKNN_DNAKNN_RNAKNNPeptideKNNProteinkNUComposition_DNAkNUComposition_RNALocalPoSpKAAFLocalPoSpKNUCF_DNALocalPoSpKNUCF_RNAmaxORFmaxORF_RNAmaxORFlength_DNAmaxORFlength_RNAMismatch_DNAMismatch_RNAMMI_DNAMMI_RNAnameKmerNCP_DNANCP_RNAneedlemannonStandardSeqNUC2Binary_DNANUC2Binary_RNANUCKpartComposition_DNANUCKpartComposition_RNAOPF_10bitOPF_7bit_T1OPF_7bit_T2OPF_7bit_T3PCPseDNCPS2_DNAPS2_RNAPS3_DNAPS3_RNAPS4_DNAPS4_RNAPSEAACPseEIIPPSEkNUCdi_DNAPSEkNUCdi_RNAPSEkNUCTri_DNAPseKRAAC_T1PseKRAAC_T10PseKRAAC_T11PseKRAAC_T12PseKRAAC_T13PseKRAAC_T14PseKRAAC_T15PseKRAAC_T16PseKRAAC_T2PseKRAAC_T3APseKRAAC_T3BPseKRAAC_T4PseKRAAC_T5PseKRAAC_T6APseKRAAC_T6BPseKRAAC_T7PseKRAAC_T8PseKRAAC_T9PSSMPSTNPdsPSTNPss_DNAPSTNPss_RNAQSOrderreadASAdirreadDisDirreadPSSMdirreadss2DirreadTorsionDirrevCompSAACSGAACSOCNumberSSEBSSECSSESTorsionAngleTPCP_DNATriNUCindex_DNAZcurve12bit_DNAZcurve12bit_RNAZcurve144bit_DNAZcurve144bit_RNAZcurve36bit_DNAZcurve36bit_RNAZcurve48bit_DNAZcurve48bit_RNAZcurve9bit_DNAZcurve9bit_RNAzSCALE

Dependencies:

Readme and manuals

Help Manual

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