Documentation

Bioinformatics Toolbox Classes

Alphabetical List By Category

High-Throughput Sequencing

Data Import

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

Alignment

BioMap Contain sequence, quality, alignment, and mapping data

Statistical Analysis

NegativeBinomialTest Unpaired hypothesis test result

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 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 Create geneont object and term objects

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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