▼Ntheplu | The Department of Theoretical Physics namespace as we define it |
▼Nyat | Yat project namespace |
►Nclassifier | Classifier related classes |
CBootstrapSampler | Class creating trainingset and validationset using bootstrapping |
CConsensusInputRanker | Robust algorithm to rank rows in a data matrix versus a target vector |
CCrossValidationSampler | Class splitting a set into training set and validation set in a crossvalidation manner |
CDataLookup1D | Class for general vector view |
CDataLookupWeighted1D | Class for general weighted vector view |
CEnsembleBuilder | Class for ensembles of supervised classifiers |
CFeatureSelector | Interface class for FeatureSelection |
CFeatureSelectorIR | FeatureSelector using an InputRanker |
CFeatureSelectorRandom | Class for selection features by random |
CGaussianKernelFunction | Class for Gaussian kernel calculations |
CIGP | Class for In Group Proportions (IGP) |
CInputRanker | Class for ranking rows in a matrix, using a Score and a target vector |
CIRRank | Functor retrieving minus rank from a InputRanker to build a ConsensusInputRanker |
CIRRetrieve | Interface class for retrieving information from a InputRanker to build a ConsensusInputRanker |
CKernel | Interface Class for Kernels |
CKernel_MEV | Memory Efficient Kernel |
CKernel_SEV | Speed Efficient Kernel |
CKernelFunction | Interface class calculating elements in Kernel |
CKernelLookup | Lookup into Kernel |
CKNN | Nearest Neighbor Classifier |
CKNN_ReciprocalDistance | A model of the concept Neighbor Weighting Method to be used with KNN to weight the votes of the k nearest neighbors of a sample |
CKNN_ReciprocalRank | A model of the concept Neighbor Weighting Method to be used with KNN to weight the votes of the k nearest neighbors of a sample |
CKNN_Uniform | A model of the concept Neighbor Weighting Method to be used with KNN to weight the votes of the k nearest neighbors of a sample |
CMatrixLookup | General view into utility::Matrix |
CMatrixLookupWeighted | General view into utility::MatrixWeighted |
CNBC | Naive Bayesian Classifier |
CNCC | Nearest Centroid Classifier |
CNeighborWeightingConcept | Concept check for a Neighbor Weighting Method |
CPerceptron | A Single-layer Perceptron |
CPolynomialKernelFunction | Class for polynomial kernel calculations |
CSampler | Interface class for dividing samples into training and validation |
CSubsetGenerator | Class splitting Data into training and validation set |
CSupervisedClassifier | Interface class for supervised classifiers that use data in a matrix format |
CSVindex | |
CSVM | Support Vector Machine |
CSvmMultiClass | Support Vector Machine for more than two classes |
CTarget | Class for containing sample labels |
►Nnormalizer | Normalization of data |
CCentralizer | Centralize a range |
CColumnNormalizer | Using a functor T to normalize each column |
CGauss | Gaussian Normalizer |
CqQuantileNormalizer | Perform Q-quantile normalization |
CQuantileNormalizer | Perform quantile normalization |
CRowNormalizer | Using a functor T to normalize each column |
CSpearman | Replace elements with normalized rank |
CZscore | Zero mean and unity variance |
►Nomic | Classes and functions related to genomics and proteomics |
CAminoAcidEqual | Functor comparing if two Codons translate to the same amino acid |
CBamFile | |
CBamHeader | Wrapper around bam_hdr_t struct |
CBamLessEnd | |
CBamLessName | |
CBamLessPos | |
CBamPair | |
CBamPairIterator | |
CBamPairProxy | |
CBamRead | Class holding a bam query |
CBamReadFilter | Filter bam reads |
CBamReadIterator | Class to iterate through a InBamFile |
CBamWriteIterator | Output iterator for bam file |
CBamWriter | |
CCodon | |
CDNA | |
CDnaComplementer | Functor that calculates genomic complement |
►CFasta | Wrapper class around struct faidx_t in libhts |
CSequence | |
CGenomicPosition | |
CGFF | |
CGFF2 | |
CGFF3 | |
CInBamFile | |
►COutBamFile | |
Cerror | Error thrown from OutBamFile::write(const BamRead&) at failure |
►CPileup | |
CEntry | |
►CVCF | |
CData | Class holiding data stored in FORMAT and data fields |
CInfo | Class handling the INFO field in an VCF entry |
►Nrandom | Random number distributions |
CBinomial | Binomial distribution |
CContinuous | Continuous random number distributions |
CContinuousGeneral | Generates numbers from a histogram in a continuous manner |
CContinuousUniform | Uniform distribution |
CDiscrete | Discrete random number distributions |
CDiscreteGeneral | General |
CDiscreteUniform | Discrete uniform distribution |
CExponential | Generator of random numbers from an exponential distribution |
CGaussian | Gaussian distribution |
CGeometric | Geomtric Distribution |
CHyperGeometric | |
CNegativeHyperGeometric | |
CPoisson | Poisson Distribution |
CRNG | Random Number Generator |
CRNG_state | Class holding state of a random generator |
►Nregression | Statistical modeling of data |
CAkimaInterpolation | Non-rounded Akima spline with natural boundary conditions |
CAkimaPeriodicInterpolation | AkimaPeriodic interpolation |
CCSplineInterpolation | Cubic spline with natural boundary conditions |
CCSplinePeriodicInterpolation | Cubic spline with periodic boundary conditions |
CGSLInterpolation | Base class for interfacing GSL interpolation |
CKernel | Interface Class for calculating the weights in a more general way than classical rectangular windows |
CKernelBox | Class for KernelBox a.k.a. rectangular window |
CKernelTriCube | Class for TriCubal kernel |
CLinear | Linear regression |
CLinearInterpolation | Linear interpolation |
CLinearWeighted | Linear regression |
CLocal | Class for Locally weighted regression |
CMultiDimensional | Linear MultiDimesional regression |
CMultiDimensionalWeighted | MultiDimesional fitting |
CMultivariate | |
CNaive | Naive Regression |
CNaiveWeighted | Naive fitting |
CNegativeBinomial | |
COneDimensional | Interface Class for One Dimensional fitting |
COneDimensionalWeighted | Interface Class for One Dimensional fitting in a weighted fashion |
CPoisson | |
CPolynomial | Polynomial regression |
CPolynomialInterpolation | Polynomial interpolation |
CPolynomialWeighted | Polynomial Regression in weighted fashion |
CTukeyBiweight | |
►Nstatistics | Statistical methods, classes, and functions |
CAUC | Area Under ROC Curve |
CAverage | Functor to take average of a range |
Caverager | |
CAverager | Class to calculate simple (first and second moments) averages |
CAverager1 | Class to calculate mean |
CAverager3 | Class to calculate 1st, 2nd, and 3rd central moments |
CAverager4 | Class to calculate 1st, 2nd, 3rd, and 4th central moments |
Caverager_base | Base class for averager classes |
Caverager_base2 | Base class for averagers calculating mean and variance |
Caverager_base3 | |
Caverager_base4 | |
Caverager_pair | |
Caverager_traits | |
Caverager_traits< utility::unweighted_iterator_tag > | |
Caverager_traits< utility::weighted_iterator_tag > | |
CAveragerPair | Class for taking care of mean and covariance of two variables |
CAveragerPairWeighted | Class for taking care of mean and covariance of two variables in a weighted manner |
CAveragerWeighted | Class to calulate averages with weights |
CChi2 | Chi squared test |
CDistance | A convenience class to implement Distance |
CEuclideanDistance | Calculates the Euclidean distance between elements of two ranges |
CFisher | Fisher's exact test |
CFoldChange | Score given by the difference by the group means |
CGaussianMixture | Data modelled as mixture of Gaussian distributions |
CHistogram | Histograms provide a convenient way of presenting the distribution of a set of data |
CKendall | Kendall's tau rank coefficient |
►CKolmogorovSmirnov | Kolmogorov Smirnov Test |
CElement | |
CKolmogorovSmirnovOneSample | Kolmogorov Smirnov Test for one class |
CLikelihoodRatioTestBinomial | Likelihood-ratio test for binomial data |
CMax | Larget element |
CMean | Mean element |
CMedian | Median element |
CMin | Smallest element |
CNth_Element | |
CPearson | Class for calculating Pearson correlation |
CPearsonCorrelation | Class for calculating Pearson correlation |
CPearsonDistance | Calculates the Pearson correlation distance between two points given by elements of ranges |
CPercentiler | Functor to calculate percentile of a range |
CROC | Reciever Operating Characteristic |
CSAMScore | Class for score used in Significance Analysis of Microarrays (SAM) |
CScore | Interface Class for score classes |
CSmoother | Estimating a distribution in a smooth fashion |
CSNRScore | Class for score based on signal-to-noise ratio (SNRScore) |
CSpearman | Spearman rank correlation coefficient |
CtScore | Class for Fisher's t-test |
CtTest | Class for Student's t-test |
CTukeyBiweightEstimator | Tukey's Biweight Estimator |
CVectorFunction | Interface Class for vector functors |
CWilcoxonFoldChange | WilcoxonFoldChange |
►Nutility | Miscellaneous functionality |
►Ndetail | |
►Nweighted_iterator | |
CTraversal | |
CBasicQueue | |
COstreamIteratorFunc | |
►Nexpression | |
CMinus | |
CMultiplies | |
CPlus | |
Cabs | |
►CAligner | Aligning two sequences |
CCigar | Compact Idiosyncratic Gapped Alignment Report |
CBasicMatrix | |
CBasicStreamRedirect | Redirect a stream to another stream |
CBasicVector | |
CCigarIterator | Iterator over a CIGAR |
Ccmd_error | Class used for error reported from Commandline or Option |
CColumnStream | |
CCommandLine | Class for parsing the command line |
Ccompose_f_gx | |
Ccompose_f_gx_hx | |
Ccompose_f_gx_hy | |
Ccompose_f_gxy | |
CContainer2D | Concept check for Container2D |
CContainer2DIterator | Iterator for a Container2D |
CDataIterator | DataIterator |
CDataIteratorConcept | Concept check for Data Iterator |
CDataWeight | Holds a pair of data and associated weight |
CDataWeightProxy | Proxy class for DataWeight |
CDeleter | Functor that deletes an object |
CDereferencer | Adaptor between pointer and pointee interface |
CDiagonalMatrix | Diagonal Matrix |
CDistanceConcept | Concept check for a Distance |
Cerrno_error | Class that contains information reported via global variable errno |
CExp | |
CFileUtil | Checking file/directory existence and access permissions |
Cget_error | Error class used in get(const std::map<Key, Tp, Compare, Alloc>& m, const Key& k) |
CGetlineIterator | Read from std::istream with std::getline |
CGSL_error | Class for errors reported from underlying GSL calls |
CIdentity | Identity functor that returns its argument |
CIndex | Class for storing indices of, e.g., a MatrixLookup |
CIO_error | Class to report errors associated with IO operations |
Citerator_traits | |
CKernelMatrix | A KernelMatrix is a Container2D |
CKernelPCA | Principal Component Analysis on a Kernel Matrix |
CkNNI | KNNimpute |
Cless_nan | Functor that behaves like std::less with the exception that it treats NaN as a number larger than infinity |
Cless_nan< DataWeight > | Specialization for DataWeight |
CLog | |
CMatrix | Interface to GSL matrix |
CMatrixExpression | An expression that can be converted to a Matrix |
CMatrixWeighted | Weighted Matrix |
CMergeIterator | Iterate over several ranges as if ranges have been merged |
CMutable_Container2D | Concept check for Mutable Container2D |
CNNI | Interface class for nearest neighbour imputation (NNI) algorithms |
COption | Container of variables for an option |
COptionArg | Option with argument |
COptionFile | Class for file related options |
COptionHelp | Class for help option |
COptionInFile | Class for file related options |
COptionOutFile | Class for file related options |
COptionSwitch | Class for switch option |
COstreamIterator | |
Cpair_value_compare | Functor comparing pairs using second |
CPairFirst | Functor that return std::pair.first |
CPairSecond | Functor that return std::pair.second |
CPCA | Principal Component Analysis |
CPriorityQueue | Multi-thread safe priority queue |
CQueue | Multi-thread safe queue |
CRange | A class for storing a shallow copy of a Range |
Cruntime_error | Class used for all runtime error detected within yat library |
►CScheduler | Handle a number of jobs and send them to threads |
CJob | |
CSegment | Class for a Segment or Interval |
CSegmentCompare | Functor using compare |
CSegmentMap | Map of Segments |
CSegmentSet | Set of Segments |
CSegmentTree | Base Class for SegmentSet and SegmentMap |
CSmartPtr | |
CSmithWaterman | |
CStrideIterator | Adaptor using a stride on underlying iterator |
CSVD | Singular Value Decomposition |
CTrivialIterator | Concept check for Trivial Iterator |
CTypeInfo | Wrapper class for storing std::type_info |
Cunweighted_iterator_tag | |
CVector | This is the yat interface to GSL vector |
CVectorBase | This is the yat interface to GSL vector |
CVectorConstView | Read-only view |
CVectorExpression | An expression that can be converted to a Vector |
CVectorMutable | This is the mutable interface to GSL vector |
CVectorView | This is the yat interface to gsl_vector_view |
Cweighted_if_any2 | |
Cweighted_if_any3 | |
Cweighted_iterator_tag | |
Cweighted_iterator_traits | |
CWeightedIterator | WeightedIterator |
CWeightedIteratorArchetype | |
CWeightedIteratorArchetype_ctor_arg | |
CWeightIterator | WeightIterator |
CWeNNI | Weighted Nearest Neighbour Imputation |