 theplu | The Department of Theoretical Physics namespace as we define it |
  yat | Yat project namespace |
   classifier | Classifier related classes |
    BootstrapSampler | Class creating trainingset and validationset using bootstrapping |
    ConsensusInputRanker | Robust algorithm to rank rows in a data matrix versus a target vector |
    CrossValidationSampler | Class splitting a set into training set and validation set in a crossvalidation manner |
    DataLookup1D | Class for general vector view |
    DataLookupWeighted1D | Class for general weighted vector view |
    EnsembleBuilder | Class for ensembles of supervised classifiers |
    FeatureSelector | Interface class for FeatureSelection |
    FeatureSelectorIR | FeatureSelector using an InputRanker |
    FeatureSelectorRandom | Class for selection features by random |
    GaussianKernelFunction | Class for Gaussian kernel calculations |
    IGP | Class for In Group Proportions (IGP) |
    IRRank | Functor retrieving minus rank from a InputRanker to build a ConsensusInputRanker |
    IRRetrieve | Interface class for retrieving information from a InputRanker to build a ConsensusInputRanker |
    InputRanker | Class for ranking rows in a matrix, using a Score and a target vector |
    Kernel | Interface Class for Kernels |
    KernelFunction | Interface class calculating elements in Kernel |
    KernelLookup | Lookup into Kernel |
    Kernel_MEV | Memory Efficient Kernel |
    Kernel_SEV | Speed Efficient Kernel |
    KNN | Nearest Neighbor Classifier |
    NeighborWeightingConcept | Concept check for a Neighbor Weighting Method |
    KNN_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 |
    KNN_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 |
    KNN_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 |
    MatrixLookup | General view into utility::Matrix |
    MatrixLookupWeighted | General view into utility::MatrixWeighted |
    NBC | Naive Bayesian Classifier |
    NCC | Nearest Centroid Classifier |
    PolynomialKernelFunction | Class for polynomial kernel calculations |
    SVM | Support Vector Machine |
    SvmMultiClass | Support Vector Machine for more than two classes |
    SVindex | |
    Sampler | Interface class for dividing samples into training and validation |
    SubsetGenerator | Class splitting Data into training and validation set |
    SupervisedClassifier | Interface class for supervised classifiers that use data in a matrix format |
    Target | Class for containing sample labels |
   normalizer | Normalization of data |
    Centralizer | Centralize a range |
    ColumnNormalizer | Using a functor T to normalize each column |
    Gauss | Gaussian Normalizer |
    qQuantileNormalizer | Perform Q-quantile normalization |
    QuantileNormalizer | Perform quantile normalization |
    RowNormalizer | Using a functor T to normalize each column |
    Spearman | Replace elements with normalized rank |
    Zscore | Zero mean and unity variance |
   omic | Classes and functions related to genomics and proteomics |
    BamFile | |
    InBamFile | |
    OutBamFile | |
     error | Error thrown from OutBamFile::write(const BamRead&) at failure |
    BamHeader | Wrapper around bam_hdr_t struct |
    BamPair | |
    BamPairProxy | |
    BamPairIterator | |
    BamRead | Class holding a bam query |
    BamLessPos | |
    BamLessEnd | |
    BamLessName | |
    BamReadFilter | Filter bam reads |
    BamReadIterator | Class to iterate through a InBamFile |
    BamWriter | |
    BamWriteIterator | Output iterator for bam file |
    Codon | |
    AminoAcidEqual | Functor comparing if two Codons translate to the same amino acid |
    DNA | |
    DnaComplementer | Functor that calculates genomic complement |
    Fasta | Wrapper class around struct faidx_t in libhts |
     Sequence | |
    GenomicPosition | |
    GFF | |
    GFF2 | |
    GFF3 | |
    Pileup | |
     Entry | |
   random | Random number distributions |
    RNG | Random Number Generator |
    RNG_state | Class holding state of a random generator |
    Discrete | Discrete random number distributions |
    Binomial | Binomial distribution |
    DiscreteGeneral | General |
    DiscreteUniform | Discrete uniform distribution |
    Geometric | Geomtric Distribution |
    HyperGeometric | |
    NegativeHyperGeometric | |
    Poisson | Poisson Distribution |
    Continuous | Continuous random number distributions |
    ContinuousUniform | Uniform distribution |
    ContinuousGeneral | Generates numbers from a histogram in a continuous manner |
    Exponential | Generator of random numbers from an exponential distribution |
    Gaussian | Gaussian distribution |
   regression | Statistical modeling of data |
    AkimaInterpolation | Non-rounded Akima spline with natural boundary conditions |
    AkimaPeriodicInterpolation | AkimaPeriodic interpolation |
    CSplineInterpolation | Cubic spline with natural boundary conditions |
    CSplinePeriodicInterpolation | Cubic spline with periodic boundary conditions |
    GSLInterpolation | Base class for interfacing GSL interpolation |
    Kernel | Interface Class for calculating the weights in a more general way than classical rectangular windows |
    KernelBox | Class for KernelBox a.k.a. rectangular window |
    KernelTriCube | Class for TriCubal kernel |
    Linear | Linear regression |
    LinearInterpolation | Linear interpolation |
    LinearWeighted | Linear regression |
    Local | Class for Locally weighted regression |
    MultiDimensional | MultiDimesional fitting |
    MultiDimensionalWeighted | MultiDimesional fitting |
    Naive | Naive Regression |
    NaiveWeighted | Naive fitting |
    OneDimensional | Interface Class for One Dimensional fitting |
    OneDimensionalWeighted | Interface Class for One Dimensional fitting in a weighted fashion |
    Polynomial | Polynomial regression |
    PolynomialInterpolation | Polynomial interpolation |
    PolynomialWeighted | Polynomial Regression in weighted fashion |
    TukeyBiweight | |
   statistics | Statistical methods, classes, and functions |
    AUC | Area Under ROC Curve |
    averager_base | Base class for averager classes |
    averager_base2 | Base class for averagers calculating mean and variance |
    averager_base3 | |
    averager_base4 | |
    Average | Functor to take average of a range |
    Averager | Class to calculate simple (first and second moments) averages |
    Averager1 | Class to calculate mean |
    Averager3 | Class to calculate 1st, 2nd, and 3rd central moments |
    Averager4 | Class to calculate 1st, 2nd, 3rd, and 4th central moments |
    AveragerPair | Class for taking care of mean and covariance of two variables |
    AveragerWeighted | Class to calulate averages with weights |
    AveragerPairWeighted | Class for taking care of mean and covariance of two variables in a weighted manner |
    averager_traits | |
    averager_traits< utility::unweighted_iterator_tag > | |
    averager_traits< utility::weighted_iterator_tag > | |
    averager | |
    averager_pair | |
    Distance | A convenience class to implement Distance |
    EuclideanDistance | Calculates the Euclidean distance between elements of two ranges |
    Fisher | Fisher's exact test |
    FoldChange | Score given by the difference by the group means |
    Histogram | Histograms provide a convenient way of presenting the distribution of a set of data |
    Kendall | Kendall's tau rank coefficient |
    KolmogorovSmirnov | Kolmogorov Smirnov Test |
     Element | |
    KolmogorovSmirnovOneSample | Kolmogorov Smirnov Test for one class |
    LikelihoodRatioTestBinomial | Likelihood-ratio test for binomial data |
    Pearson | Class for calculating Pearson correlation |
    PearsonCorrelation | Class for calculating Pearson correlation |
    PearsonDistance | Calculates the Pearson correlation distance between two points given by elements of ranges |
    Percentiler | Functor to calculate percentile of a range |
    ROC | Reciever Operating Characteristic |
    SAMScore | Class for score used in Significance Analysis of Microarrays (SAM) |
    Score | Interface Class for score classes |
    Smoother | Estimating a distribution in a smooth fashion |
    SNRScore | Class for score based on signal-to-noise ratio (SNRScore) |
    Spearman | Spearman rank correlation coefficient |
    TukeyBiweightEstimator | Tukey's Biweight Estimator |
    tScore | Class for Fisher's t-test |
    tTest | Class for Student's t-test |
    VectorFunction | Interface Class for vector functors |
    Max | Larget element |
    Median | Median element |
    Mean | Mean element |
    Min | Smallest element |
    Nth_Element | |
    WilcoxonFoldChange | WilcoxonFoldChange |
   utility | Miscellaneous functionality |
    detail | |
     weighted_iterator | |
      Traversal | |
     OstreamIteratorFunc | |
    Aligner | Aligning two sequences |
     Cigar | Compact Idiosyncratic Gapped Alignment Report |
    CigarIterator | Iterator over a CIGAR |
    ColumnStream | |
    CommandLine | Class for parsing the command line |
    Container2D | Concept check for Container2D |
    Mutable_Container2D | Concept check for Mutable Container2D |
    TrivialIterator | Concept check for Trivial Iterator |
    DataIteratorConcept | Concept check for Data Iterator |
    DistanceConcept | Concept check for a Distance |
    Container2DIterator | Iterator for a Container2D |
    DataIterator | DataIterator |
    DataWeight | Holds a pair of data and associated weight |
    DataWeightProxy | Proxy class for DataWeight |
    Deleter | Functor that deletes an object |
    runtime_error | Class used for all runtime error detected within yat library |
    cmd_error | Class used for error reported from Commandline or Option |
    errno_error | Class that contains information reported via global variable errno |
    GSL_error | Class for errors reported from underlying GSL calls |
    IO_error | Class to report errors associated with IO operations |
    FileUtil | Checking file/directory existence and access permissions |
    GetlineIterator | Read from std::istream with std::getline |
    Index | Class for storing indices of, e.g., a MatrixLookup |
    unweighted_iterator_tag | |
    weighted_iterator_tag | |
    weighted_iterator_traits | |
    weighted_if_any2 | |
    weighted_if_any3 | |
    iterator_traits | |
    KernelMatrix | A KernelMatrix is a Container2D |
    KernelPCA | Principal Component Analysis on a Kernel Matrix |
    kNNI | KNNimpute |
    Matrix | Interface to GSL matrix |
    MatrixWeighted | Weighted Matrix |
    MergeIterator | Iterate over several ranges as if ranges have been merged |
    NNI | Interface class for nearest neighbour imputation (NNI) algorithms |
    Option | Container of variables for an option |
    OptionArg | Option with argument |
    OptionFile | Class for file related options |
    OptionInFile | Class for file related options |
    OptionOutFile | Class for file related options |
    OptionHelp | Class for help option |
    OptionSwitch | Class for switch option |
    OstreamIterator | |
    PCA | Principal Component Analysis |
    PriorityQueue | Multi-thread safe priority queue |
    Queue | Multi-thread safe queue |
    Scheduler | Handle a number of jobs and send them to threads |
     Job | |
    Segment | Class for a Segment or Interval |
    SegmentCompare | Functor using compare |
    SegmentMap | Map of Segments |
    SegmentSet | Set of Segments |
    SegmentTree | Base Class for SegmentSet and SegmentMap |
    SmartPtr | |
    SmithWaterman | |
    BasicStreamRedirect | Redirect a stream to another stream |
    Range | A class for storing a shallow copy of a Range |
    abs | |
    Dereferencer | Adaptor between pointer and pointee interface |
    compose_f_gx_hy | |
    compose_f_gxy | |
    compose_f_gx | |
    compose_f_gx_hx | |
    Exp | |
    Identity | Identity functor that returns its argument |
    get_error | Error class used in get(const std::map<Key, Tp, Compare, Alloc>& m, const Key& k) |
    less_nan | Functor that behaves like std::less with the exception that it treats NaN as a number larger than infinity |
    less_nan< DataWeight > | Specialization for DataWeight |
    Log | |
    pair_value_compare | Functor comparing pairs using second |
    PairFirst | Functor that return std::pair.first |
    PairSecond | Functor that return std::pair.second |
    StrideIterator | Adaptor using a stride on underlying iterator |
    SVD | Singular Value Decomposition |
    TypeInfo | Wrapper class for storing std::type_info |
    Vector | This is the yat interface to GSL vector |
    VectorBase | This is the yat interface to GSL vector |
    VectorConstView | Read-only view |
    VectorMutable | This is the mutable interface to GSL vector |
    VectorView | This is the yat interface to gsl_vector_view |
    WeightedIteratorArchetype_ctor_arg | |
    WeightedIteratorArchetype | |
    WeightedIterator | WeightedIterator |
    WeightIterator | WeightIterator |
    WeNNI | Weighted Nearest Neighbour Imputation |