Man pages for crarlus/paprbag
Pathogenicity Prediction of Bacterial Genomes

AAindexDataList of 544 physicochemical and biological properties for the...
AA_PhysChemPropsObtain the physico-chemical properties from a peptide...
AApropertyAmino acid properties list of amino acid with properties...
BestUcoEstimate the Codon usage from a sequence
CheckFeaturesCheck valididity of feature table
Count.SpacedWordsCompute SpacedWords
CreateFeaturesFromReadsCreate features from reads
Create.TrainingDataSetCreate a new training data set
default.AAindexSelectionPrint the default selection of aaindices and their...
Enumerate.SpacerPatternsEnumerate all possible patterns of spacers
FindPatternsIn6framesFind patterns in all 6-frame translations of a read
FindPatternsIn6frames_wMismatchesFind patterns in all 6-frame translations of a read
FindPatternsInAAseq_wMismatchesFind patterns of amino acids
forestExample random forest
GenomicMotifsGenomic Motifs 100 most frequent 8-mers in bacterial genomes
GetAAindexStatsGet the AAindex property of a peptide sequence
GetBestTranslatedSequenceTranslate nucleotide sequence into a amino acid sequence
GetDiPeptideFrequencyGet the frequency of di-peptides
GetMonoPeptideFrequencyGet the Frequency of each amino acid
GetOligonucleotideFrequencyGet the ologonuleotide frequency
GetOSidExtract the Organism ID (PRJNA accession)
IdentifyFeatures.FromForestIdentify features from random forest object
LabelsPathogenicity labels
Make.SymmetricMake Features Symmetric by combining a dna string with its...
MatchOSlabelMatch the OSid (Bioproject id) to a vector of
Match.SymmetricPartnersMatch a DNA sequence and its reverse complement
Predict.ReadSetMake a prediction from a set of reads
Predict.ReadSet.fromFilesPredict ReadSet
prosite_Top20Prosite patterns
ReadDataExample read data
Run.TrainingThe workhorse function for the training workflow
SaveFeatureFileSave Features into Rdata file
SelectFeatureSubsetFunction to select a subset of features from the feature...
Standard.configurationStandard configuration for feature extraction
Standard.configuration_peptideStandard configuration for feature extraction including...
trainingDataExample training data Provides a small set of training Data...
UpdateFeaturesUpdate all features in a specified folder
crarlus/paprbag documentation built on June 29, 2018, 10:57 p.m.