Difference between revisions of "Tutorials"
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===[[Tutorial - Classification | Classification]]=== | ===[[Tutorial - Classification | Classification]]=== | ||
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===[[Coming Soon | Coming Soon]]=== | ===[[Coming Soon | Coming Soon]]=== | ||
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Revision as of 14:45, 12 August 2008
The tutorials shown on this page provide a quick introduction to the most important features of geWorkbench. Additional information can be found in the User Guide (in preparation) and in the Online Help section of the program.
All data sets used in the tutorials are available from the download area of our site.
Note (7/7/2008) - geWorkbench version 1.5 - The tutorials will be updated in the coming days to reflect changes made in geWorkbench version 1.5.
Getting Started
Obtaining and installing geWorkbench. Requirements.
Basics
A brief introduction to the use of geWorkbench.
Projects and Data Files
Creating projects, loading microarray data files, merging into one dataset, and saving.
Project Details
Creating projects, loading microarray data files, merging into one dataset, and saving.
Data Subsets
Subsets of both markers and arrays can be defined for targeted analysis.
Viewing a Microarray Dataset
Survey of geWorkbench visusaliztion tools for microarray data.
Filtering and Normalizing
geWorkbench provides numerous methods for filtering and normalizing microarray data.
Expression Value Distribution
View and manipulate a histogram of the distribution of expression values for each array.
Differential Expression
Several variants of the t-test are available.
Clustering
Data can be clustered using a fast hierarchical clustering routine, as well as SOMs.
Marker Annotations
Marker annotations can be retrieved, including BioCarta pathway diagrams.
Sequence Retrieval
Genomic sequences for markers can be retrieved for further analysis.
BLAST
geWorkbench can run BLAST jobs on the JCSB cluster.
Pattern Discovery
Upstream seqeunce can be analyzed for conserved sequence patterns.
Promoter Analysis
Search a set of sequences against a promoter database.
ARACNE
Formal method for reverse Engineering - microarray datasets can be analyzed for interactions between genes.
GO Term Enrichment
Determine if particluar Gene Ontology terms are overrepresented in a data subset.
Jmol
Jmol is a molecular structure viewer for viewing PDB format files.
MatrixREDUCE
Cellular Networks KnowledgeBase
Classification
Coming Soon
A Number of components are under active development.
