Documentation

Bioinformatics Toolbox Classes

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
Was this topic helpful?