AAindexData | List of 544 physicochemical and biological properties for the... |
AA_PhysChemProps | Obtain the physico-chemical properties from a peptide... |
AAproperty | Amino acid properties list of amino acid with properties... |
BestUco | Estimate the Codon usage from a sequence |
CheckFeatures | Check valididity of feature table |
Count.SpacedWords | Compute SpacedWords |
CreateFeaturesFromReads | Create features from reads |
Create.TrainingDataSet | Create a new training data set |
default.AAindexSelection | Print the default selection of aaindices and their... |
Enumerate.SpacerPatterns | Enumerate all possible patterns of spacers |
FindPatternsIn6frames | Find patterns in all 6-frame translations of a read |
FindPatternsIn6frames_wMismatches | Find patterns in all 6-frame translations of a read |
FindPatternsInAAseq_wMismatches | Find patterns of amino acids |
forest | Example random forest |
GenomicMotifs | Genomic Motifs 100 most frequent 8-mers in bacterial genomes |
GetAAindexStats | Get the AAindex property of a peptide sequence |
GetBestTranslatedSequence | Translate nucleotide sequence into a amino acid sequence |
GetDiPeptideFrequency | Get the frequency of di-peptides |
GetMonoPeptideFrequency | Get the Frequency of each amino acid |
GetOligonucleotideFrequency | Get the ologonuleotide frequency |
GetOSid | Extract the Organism ID (PRJNA accession) |
IdentifyFeatures.FromForest | Identify features from random forest object |
Labels | Pathogenicity labels |
Make.Symmetric | Make Features Symmetric by combining a dna string with its... |
MatchOSlabel | Match the OSid (Bioproject id) to a vector of |
Match.SymmetricPartners | Match a DNA sequence and its reverse complement |
Predict.ReadSet | Make a prediction from a set of reads |
Predict.ReadSet.fromFiles | Predict ReadSet |
prosite_Top20 | Prosite patterns |
ReadData | Example read data |
Run.Training | The workhorse function for the training workflow |
SaveFeatureFile | Save Features into Rdata file |
SelectFeatureSubset | Function to select a subset of features from the feature... |
Standard.configuration | Standard configuration for feature extraction |
Standard.configuration_peptide | Standard configuration for feature extraction including... |
trainingData | Example training data Provides a small set of training Data... |
UpdateFeatures | Update all features in a specified folder |
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