Classes in Bioinformatics Toolbox

  • By Category | Alphabetical List
  • High-Throughput Sequencing

    Data Import and Management

    BioIndexedFile Allow quick and efficient access to large text file with nonuniform-size entries
    BioMap Contain sequence, quality, alignment, and mapping data
    BioRead Contain sequence and quality data
    BioReadQualityStatistics Quality statistics from a short-read sequence file
    GFFAnnotation Represent General Feature Format (GFF) annotations
    GTFAnnotation Represent Gene Transfer Format (GTF) annotations

    Preprocessing

    BioMap Contain sequence, quality, alignment, and mapping data
    BioReadQualityStatistics Quality statistics from a short-read sequence file
    GFFAnnotation Represent General Feature Format (GFF) annotations
    GTFAnnotation Represent Gene Transfer Format (GTF) annotations

    RNA

    BioRead Contain sequence and quality data
    BioMap Contain sequence, quality, alignment, and mapping data
    BioReadQualityStatistics Quality statistics from a short-read sequence file
    GFFAnnotation Represent General Feature Format (GFF) annotations
    GTFAnnotation Represent Gene Transfer Format (GTF) annotations
    NegativeBinomialTest Unpaired hypothesis test result
    HeatMap Display heat map of matrix data and create HeatMap object
    HeatMap object Object containing matrix and heat map display properties
    clustergram Compute hierarchical clustering, display dendrogram and heat map, and create clustergram object
    clustergram object Object containing hierarchical clustering analysis data
    DataMatrix Create DataMatrix object
    DataMatrix object Data structure encapsulating data and metadata from microarray experiment so that it can be indexed by gene or probe identifiers and by sample identifiers

    DNA

    BioRead Contain sequence and quality data
    BioMap Contain sequence, quality, alignment, and mapping data
    BioReadQualityStatistics Quality statistics from a short-read sequence file
    GFFAnnotation Represent General Feature Format (GFF) annotations
    GTFAnnotation Represent Gene Transfer Format (GTF) annotations

    Gene Ontology

    geneont Data structure containing Gene Ontology (GO) information

    Network Analysis and Visualization

    biograph Create biograph object
    biograph object Data structure containing generic interconnected data used to implement directed graph

    Microarray Analysis

    Data Import and Management

    bioma.ExpressionSet Contain data from microarray gene expression experiment
    bioma.data.ExptData Contain data values from microarray experiment
    bioma.data.MetaData Contain metadata from microarray experiment
    bioma.data.MIAME Contain experiment information from microarray gene expression experiment

    Expression Analysis

    DataMatrix Create DataMatrix object
    DataMatrix object Data structure encapsulating data and metadata from microarray experiment so that it can be indexed by gene or probe identifiers and by sample identifiers
    bioma.ExpressionSet Contain data from microarray gene expression experiment
    bioma.data.ExptData Contain data values from microarray experiment
    bioma.data.MetaData Contain metadata from microarray experiment
    bioma.data.MIAME Contain experiment information from microarray gene expression experiment
    NegativeBinomialTest Unpaired hypothesis test result
    HeatMap Display heat map of matrix data and create HeatMap object
    HeatMap object Object containing matrix and heat map display properties
    clustergram Compute hierarchical clustering, display dendrogram and heat map, and create clustergram object
    clustergram object Object containing hierarchical clustering analysis data

    Genetic Variant Analysis

    DataMatrix Create DataMatrix object
    DataMatrix object Data structure encapsulating data and metadata from microarray experiment so that it can be indexed by gene or probe identifiers and by sample identifiers
    NegativeBinomialTest Unpaired hypothesis test result

    Gene Ontology

    geneont Data structure containing Gene Ontology (GO) information

    Network Analysis and Visualization

    biograph Create biograph object
    biograph object Data structure containing generic interconnected data used to implement directed graph

    Sequence Analysis

    Phylogenetic Analysis

    phytree Create phytree object
    phytree object Data structure containing phylogenetic tree
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