Difference between revisions of "Tutorials"
Line 14: Line 14:
 
===[[Tutorial - Basics | Basics]]===
 
===[[Tutorial - Basics | Basics]]===
 
A brief introduction to the use of geWorkbench.
 
A brief introduction to the use of geWorkbench.
 +
 +
===[[Tutorial - Data | Tutorial Data]]===
 +
 +
===[[Tutorial - Data Subsets | Data Subsets]]===
 +
Subsets of both markers and arrays can be defined for targeted analysis.
  
 
===[[Tutorial - Projects and Data Files | Projects and Data Files]]===
 
===[[Tutorial - Projects and Data Files | Projects and Data Files]]===
Line 19: Line 24:
  
 
===[[Tutorial - Project Details | Project Details]]===
 
===[[Tutorial - Project Details | Project Details]]===
−
Creating projects, loading microarray data files, merging into one dataset, and saving.
 
  
−
===[[Tutorial - Data Subsets | Data Subsets]]===
+
 
−
Subsets of both markers and arrays can be defined for targeted analysis.
+
===[[Tutorial - Local Data Files | Local Data Files]]===
 +
 
 +
 
 +
===[[Tutorial - Remote Data Sources | Remote Data Sources (caArray)]]===
 +
 
  
 
===[[Tutorial - Viewing a Microarray Dataset | Viewing a Microarray Dataset]]===
 
===[[Tutorial - Viewing a Microarray Dataset | Viewing a Microarray Dataset]]===
 
Survey of geWorkbench visusaliztion tools for microarray data.
 
Survey of geWorkbench visusaliztion tools for microarray data.
  
−
===[[Tutorial - Filtering and Normalizing | Filtering and Normalizing]]===
 
−
geWorkbench provides numerous methods for filtering and normalizing microarray data.
 
  
−
===[[Tutorial - EVD | Expression Value Distribution]]===
+
===[[Tutorial - ARACNE | ARACNE]]===
−
View and manipulate a histogram of the distribution of expression values for each array.
+
Formal method for reverse Engineering - microarray datasets can be analyzed for interactions between genes.
 +
 
 +
===[[Tutorial - BLAST | BLAST]]===
 +
geWorkbench can run BLAST jobs on the JCSB cluster.
  
−
===[[Tutorial - Differential Expression | Differential Expression]]===
+
===[[Tutorial - Cellular Networks KnowledgeBase | Cellular Networks KnowledgeBase]]===
−
Several variants of the t-test are available.
 
  
−
===[[Tutorial - Clustering | Clustering]]===
 
−
Data can be clustered using a fast hierarchical clustering routine, as well as SOMs.
 
  
−
===[[Tutorial - Marker Annotations | Marker Annotations]]===
+
===[[Tutorial - Classification | Classification]]===
−
Marker annotations can be retrieved, including BioCarta pathway diagrams.
 
  
−
===[[Tutorial - Sequence Retrieval | Sequence Retrieval]]===
 
−
Genomic sequences for markers can be retrieved for further analysis.
 
  
−
===[[Tutorial - BLAST | BLAST]]===
+
===[[Tutorial - Clustering | Clustering]]===
−
geWorkbench can run BLAST jobs on the JCSB cluster.
+
Data can be clustered using a fast hierarchical clustering routine, as well as SOMs.
  
−
===[[Tutorial - Pattern Discovery | Pattern Discovery]]===
+
===[[Tutorial - Differential Expression | Differential Expression]]===
−
Upstream seqeunce can be analyzed for conserved sequence patterns.
+
Several variants of the t-test are available.
  
−
===[[Tutorial - Promoter Analysis | Promoter Analysis]]===
+
===[[Tutorial - EVD | Expression Value Distribution]]===
−
Search a set of sequences against a promoter database.
+
View and manipulate a histogram of the distribution of expression values for each array.
  
−
===[[Tutorial - ARACNE | ARACNE]]===
+
===[[Tutorial - Filtering and Normalizing | Filtering and Normalizing]]===
−
Formal method for reverse Engineering - microarray datasets can be analyzed for interactions between genes.
+
geWorkbench provides numerous methods for filtering and normalizing microarray data.
  
 
===[[Tutorial - GO Term Enrichment | GO Term Enrichment]]===
 
===[[Tutorial - GO Term Enrichment | GO Term Enrichment]]===
−
Determine if particluar Gene Ontology terms are overrepresented in a data subset.
+
Not in current releases.  
  
 
===[[Tutorial - Jmol | Jmol]]===
 
===[[Tutorial - Jmol | Jmol]]===
 
Jmol is a molecular structure viewer for viewing PDB format files.
 
Jmol is a molecular structure viewer for viewing PDB format files.
 +
 +
===[[Tutorial - Marker Annotations | Marker Annotations]]===
 +
Marker annotations can be retrieved, including BioCarta pathway diagrams.
  
 
===[[Tutorial - MatrixREDUCE | MatrixREDUCE]]===
 
===[[Tutorial - MatrixREDUCE | MatrixREDUCE]]===
  
  
 +
===[[Tutorial - MINDy| MINDy]]===
 +
 +
 +
===[[Tutorial - Pattern Discovery | Pattern Discovery]]===
 +
Upstream seqeunce can be analyzed for conserved sequence patterns.
  
−
===[[Tutorial - Cellular Networks KnowledgeBase | Cellular Networks KnowledgeBase]]===
+
===[[Tutorial - Promoter Analysis | Promoter Analysis]]===
 +
Search a set of sequences against a promoter database.
  
  
 +
===[[Tutorial - Sequence Retrieval | Sequence Retrieval]]===
 +
Genomic sequences for markers can be retrieved for further analysis.
  
−
===[[Tutorial - Classification | Classification]]===
 
  
  
−
===[[Tutorial_-_ANOVA | ANOVA]]===
 
−
coming soon.
 
  
 +
===Coming Soon===
 +
Tutorials for a number of components are under active development.
  
−
===[[Coming Soon | Coming Soon]]===
+
====[[Tutorial_-_ANOVA | ANOVA]]====
−
A Number of components are under active development.
 

Revision as of 13:37, 10 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 (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.


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.

BLAST

geWorkbench can run BLAST jobs on the JCSB cluster.

Cellular Networks KnowledgeBase

Classification

Clustering

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

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 active development.

ANOVA

Retrieved from "http://wiki.c2b2.columbia.edu/workbench/index.php?title=Tutorials&oldid=4918"