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R2011b Documentation → Bioinformatics Toolbox
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Contents

Index

• Getting Started

Required Software

Optional Software

Data Formats and Databases

Sequence Alignments

Sequence Utilities and Statistics

Protein Property Analysis

Phylogenetic Analysis

Microarray Data Analysis

Microarray Data Storage

Mass Spectrometry Data Analysis

Graph Theory Functions

Graph Visualization

Statistical Learning and Visualization

Prototyping and Development Environment

Data Visualization

Algorithm Sharing and Application Deployment

Using Excel and MATLAB Together

About the Example

Before Running the Example

Running the Example for the Entire Data Set

Editing Formulas to Run the Example on a Subset of the Data

Using the Spreadsheet Link EX Interface to Interact With the Data in MATLAB

What Are get Functions?

Creating the getpubmed Function

Understanding Support Vector Machines

Using Support Vector Machines

Example: Nonlinear Classifier with Gaussian Kernel

Example: SVM Classification with Cross Validation

• User's Guide

• High-Throughput Sequence Analysis

• Sequence Analysis

• Microarray Analysis

Storing and Managing Gene Expression Data in Objects

• Representing Expression Data Values in DataMatrix Objects

Overview of DataMatrix Objects

Constructing DataMatrix Objects

Getting and Setting Properties of a DataMatrix Object

Accessing Data in DataMatrix Objects

• Representing Expression Data Values in ExptData Objects

Overview of ExptData Objects

Constructing ExptData Objects

Using Properties of an ExptData Object

Using Methods of an ExptData Object

• Representing Sample and Feature Metadata in MetaData Objects

Overview of MetaData Objects

Constructing MetaData Objects

Using Properties of a MetaData Object

Using Methods of a MetaData Object

• Representing Experiment Information in a MIAME Object

Overview of MIAME Objects

Constructing MIAME Objects

Using Properties of a MIAME Object

Using Methods of a MIAME Object

• Representing All Data and Information in an ExpressionSet Object

Overview of ExpressionSet Objects

Constructing ExpressionSet Objects

Using Properties of an ExpressionSet Object

Using Methods of an ExpressionSet Object

• Example: Visualizing Microarray Images

Overview of the Mouse Example

Exploring the Microarray Data Set

Spatial Images of Microarray Data

Statistics of the Microarrays

Scatter Plots of Microarray Data

• Example: Analyzing Gene Expression Profiles

Overview of the Yeast Example

Exploring the Data Set

Filtering Genes

Clustering Genes

Principal Component Analysis

Detecting DNA Copy Number Alteration in Array-Based CGH Data

Exploring Gene Expression Data

• Phylogenetic Analysis

• Release Notes

Microarray Analysis

Viewing and Aligning Multiple Sequences

Viewing and Aligning Multiple Sequences

Storing and Managing Gene Expression Data in Objects

Storing and Managing Gene Expression Data in Objects

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