Man pages for crarlus/paprbag
Pathogenicity Prediction of Bacterial Genomes
| 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 |
