geWorkbench

Revision as of 18:19, 14 July 2009

Home \| Quick Start \| Basics \| Menu Bar \| Preferences \| Component Configuration Manager \| Workspace \| Information Panel \| Local Data Files \| File Formats \| caArray \| Array Sets \| Marker Sets \| Microarray Dataset Viewers \| Filtering \| Normalization \| Tutorial Data \| geWorkbench-web Tutorials	Analysis Framework \| ANOVA \| ARACNe \| BLAST \| Cellular Networks KnowledgeBase \| CeRNA/Hermes Query \| Classification (KNN, WV) \| Color Mosaic \| Consensus Clustering \| Cytoscape \| Cupid \| DeMAND \| Expression Value Distribution \| Fold-Change \| Gene Ontology Term Analysis \| Gene Ontology Viewer \| GenomeSpace \| genSpace \| Grid Services \| GSEA \| Hierarchical Clustering \| IDEA \| Jmol \| K-Means Clustering \| LINCS Query \| Marker Annotations \| MarkUs \| Master Regulator Analysis \| (MRA-FET Method) \| (MRA-MARINa Method) \| MatrixREDUCE \| MINDy \| Pattern Discovery \| PCA \| Promoter Analysis \| Pudge \| SAM \| Sequence Retriever \| SkyBase \| SkyLine \| SOM \| SVM \| T-Test \| Viper Analysis \| Volcano Plot

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 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.

Current components

Getting Started

Obtaining and installing geWorkbench. Requirements.

Basics

A brief introduction to the use of geWorkbench.

Tutorial Data

Data Subsets

Subsets of both markers and arrays can be defined for targeted analysis.

Projects and Data Files

Creating projects, loading microarray data files, merging into one dataset, and saving.

Project Details

Local Data Files

Remote Data Sources (caArray)

Viewing a Microarray Dataset

Survey of geWorkbench visusaliztion tools for microarray data.

ARACNE

Formal method for reverse Engineering - microarray datasets can be analyzed for interactions between genes. Now includes new ARACNe2, which implements the much faster Adaptive Partitioning algorithm and accurate parameter estimation.

BLAST

Submits BLAST jobs to the NCBI server and displays and allows further interaction with alignment results.

Cellular Networks KnowledgeBase

Classification

Clustering

Data can be clustered using a fast hierarchical clustering routine, as well as SOMs.

Cytoscape

Cytoscape is used to display network interaction diagrams (from adjacency matrices). It features two-way interaction with the geWorkbench Markers component.

Differential Expression

Several variants of the t-test are available.

Expression Value Distribution

View and manipulate a histogram of the distribution of expression values for each array.

Filtering and Normalizing

geWorkbench provides numerous methods for filtering and normalizing microarray data.

GO Term Enrichment

Not in current releases.

Jmol

Jmol is a molecular structure viewer for viewing PDB format files.

Marker Annotations

Marker annotations can be retrieved, including BioCarta pathway diagrams.

MatrixREDUCE

MINDy

Pattern Discovery

Upstream seqeunce can be analyzed for conserved sequence patterns.

Promoter Analysis

Search a set of sequences against a promoter database.

Sequence Retrieval

Genomic sequences for markers can be retrieved for further analysis.

Coming Soon

Tutorials for a number of components are under development, including:

ANOVA
caGrid v1.3 - How the geWorkbench grid services are set up using caTransfer.
Expression Profiles
Sequence (Viewer)

Marker Annotations - will be updated to add Cancer Gene Index integration.

Gene Pattern components:

PCA (GenePattern) - Analysis and Viewer
K-nearest neighbors (GenePattern)
SVM 3.0 (GenePattern) - Analysis and Viewer - include, we need to develop online help and tutorial (Aris).
WV - Weighted Voting (GenePattern)

@@ Line 99: / Line 99: @@
 * caGrid v1.3 - How the geWorkbench grid services are set up using caTransfer.
 * Expression Profiles
-* MRA - Master Regulator Analysis
 * Sequence (Viewer)