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Bioinformatics Toolbox Classes

Alphabetical List By Category

High-Throughput Sequencing

Data Import

BioReadContain sequence and quality data
BioMapContain sequence, quality, alignment, and mapping data
BioReadQualityStatisticsQuality statistics from a short-read sequence file
BioIndexedFileAllow quick and efficient access to large text file with nonuniform-size entries
GFFAnnotationContain General Feature Format (GFF) annotations
GTFAnnotationContain Gene Transfer Format (GTF) annotations

Alignment

BioMapContain sequence, quality, alignment, and mapping data

Statistical Analysis

NegativeBinomialTestUnpaired hypothesis test result

Microarray Analysis

Data Import and Management

bioma.ExpressionSetContain data from microarray gene expression experiment
bioma.data.ExptDataContain data values from microarray experiment
bioma.data.MetaDataContain metadata from microarray experiment
bioma.data.MIAMEContain experiment information from microarray gene expression experiment

Expression Analysis

DataMatrixCreate DataMatrix object
DataMatrix objectData structure encapsulating data and metadata from microarray experiment so that it can be indexed by gene or probe identifiers and by sample identifiers
bioma.ExpressionSetContain data from microarray gene expression experiment
bioma.data.ExptDataContain data values from microarray experiment
bioma.data.MetaDataContain metadata from microarray experiment
bioma.data.MIAMEContain experiment information from microarray gene expression experiment
NegativeBinomialTestUnpaired hypothesis test result
HeatMapDisplay heat map of matrix data and create HeatMap object
HeatMap objectObject containing matrix and heat map display properties
clustergram objectObject containing hierarchical clustering analysis data

Genetic Variant Analysis

DataMatrixCreate DataMatrix object
DataMatrix objectData structure encapsulating data and metadata from microarray experiment so that it can be indexed by gene or probe identifiers and by sample identifiers
NegativeBinomialTestUnpaired hypothesis test result

Gene Ontology

geneontCreate geneont object and term objects

Network Analysis and Visualization

biographCreate biograph object
biograph objectData structure containing generic interconnected data used to implement directed graph

Sequence Analysis

Phylogenetic Analysis

phytreeCreate phytree object
phytree objectData structure containing phylogenetic tree
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