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Ymir
.9
Fast\C++toolforcomputationofassemblingprobabilities,statisticalinferenceofassemblingstatisticalmodelandgenerationofartificialsequencesofT-cellreceptorsdata.
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Ymir
.9
Fast\C++toolforcomputationofassemblingprobabilities,statisticalinferenceofassemblingstatisticalmodelandgenerationofartificialsequencesofT-cellreceptorsdata.
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| ▼NJson | |
| CBuiltStyledStreamWriter | |
| CCommentStyle | Scoped enums are not available until C++11 |
| CException | |
| CLogicError | |
| COurCharReader | |
| COurFeatures | |
| ▼COurReader | |
| CStructuredError | |
| CRuntimeError | |
| ▼Nymir | |
| CAbstractInsertionModel | Class for representing VJ / VD / DJ insertions models - either a mono-nucleotide or a di-nucleotide model |
| CAbstractTDContainer | |
| CAlignmentBase | |
| CAlignmentColumnOptions | |
| CAlignmentEventScore | |
| CAlignmentMatrixBase | |
| CAlignmentVectorBase | |
| CCDR3AlignerFunctor_D | |
| CCDR3AlignerFunctor_J | |
| CCDR3AlignerFunctor_V | |
| CCloneset | |
| CClonesetView | |
| CClonotype | |
| CClonotypeAssembler | |
| CClonotypeBuilder | |
| ▼CCodonTable | A struct for representing nucleotide codons for amino acids |
| CCodons | |
| CDiNucInsertionModel | |
| CEMAlgorithm | Implementation of the EM-algorithm for statistical inference of assembling model parameters. Classic version described in (Murugan et al 2012) |
| CForwardBackwardAlgorithm | |
| CGappedAlignment | |
| CGappedAlignmentVector | |
| ▼CGeneSegmentAlphabet | |
| CGeneSegment | |
| CMAAG | Multi-Alignment Assembly Graph - basic class for representing all possible generation scenarios of a nucleotide or amino acid sequence of an immune receptor |
| CMAAGBuilder | |
| CMAAGForwardBackwardAlgorithm | |
| CMatrix | Simple matrix class |
| CModelParameterVector | Class for storing parameters of assembling statistical model. Note: event with index 0 (zero) is "null" event and always has zero probability. Vector is ordered so for VJ or VDJ recombination specific family events stored in specific order |
| CModelParser | |
| CMonoNucInsertionModel | |
| ▼CMultiMatrixChain | Class for storing lists of matrices, where one node in the list (called "chain") could contain more than one matrix |
| CNode | Node in the chain. Stores one or more matrices with equal size |
| CNaiveCDR3AlignerFunctor_D | |
| CNaiveCDR3AlignerFunctor_J | |
| CNaiveCDR3AlignerFunctor_V | |
| CNoGapAlignment | |
| CNoGapAlignmentVector | |
| CProbabilisticAssemblingModel | |
| CRepertoireParser | Parser for text files with repertoire data. By default it's MiTCR parser. To make new parsers inherit from this class and rewrite virtual private method "parseRepertoire" |
| CRepertoireParserStatistics | |
| CRepertoireWriter | |
| CSGAlgorithm | |
| ▼CStatisticalInferenceAlgorithm | Interface for algorithms for statistical inference of assembling model parameters |
| CAlgorithmParameters | |
| CSWAlignerFunctor_D | |
| CSWAlignerFunctor_VJ | |
| CSWNGAlignerFunctor_D | |
| CSWNGAlignerFunctor_J | |
| CSWNGAlignerFunctor_V | |
| CTDMatrix | |
| CTDMatrixList | |
| CTDVector | Vector of gene segments |
| CTDVectorList | List of std::vectors for deletions and insertions |
| CTestInfo | |
| CVD2JForwardBackward | |
| CVDJAlignerBase | |
| CVDJAlignerParameters | |
| CVDJAlignment | |
| CVDJAlignmentBuilder | |
| CVDJAlignmentEventScore | |
| CVDJAlignmentScoreThreshold | |
| CVDJForwardBackward | |
| CVDJModelParser | |
| CVDJRecombinationGenes | |
| CVJForwardBackward | |
| CVJModelParser | |
| CBlockEMAlgorithm | Implementation of the online EM-algorithm for statistical inference of assembling model parameters |
| CEventIndMatrixChain | Class for storing chain of matrices of indices of scenario events |
| CNumErrorsMMC | Class for storing a number of errors for each scenario event |
| CProbMatrixChain | Class for storing chain of matrices of scenario event probabilities |
1.8.11
