Agilent | Software Extras - GeneSpring GX Software

GeneSpring GX Extras are useful additions to GeneSpring GX software. This page consists of two sections: GeneSpring GX 9/10 and GeneSpring GX 7.

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GeneSpring GX 9/10

Documentation

GeneSpring GX 9 Quick Start Guide GeneSpring GX 10 Quick Start Guide GeneSpring GX 9 User Manual GeneSpring GX 9/10 Tutorials

Statistical Analysis Comparison This document presents the differing analysis comparisons between GeneSpring GX 7.3.1 and GeneSpring GX 9/10.		Comparison of Normalized Values This document presents a detailed comparison of the normalized values resulting from the Median Shift and Baseline transformation to median method in GeneSpring GX 9/10 and the Per Chip: to median and Per Gene: to median method of GeneSpring GX 7.3.1. The effects of differences on downstream analysis are also presented.

Licenses

GeneSpring GX 9/10 Floating License Server The floating license server allows for the concurrent use of GeneSpring GX 9/10 and later.

Databases

GeneSpring GX 9/10 Dataset for Affymetrix Tutorial Download a zip file containing the Congestive Heart Failure gene expression microarray dataset to be used with the GeneSpring GX 9/10 Data Analysis Tutorial for Affymetrix data. TargetScan script and User Guide GeneSpring GX – TargetScan integration facilitates the identification of the target genes regulated by miRNAs by the use of the TargetScan database integrated with GeneSpring GX.		GeneSpring GX 9/10 Dataset for Agilent Tutorial Download a zip file containing the VSMC Cytokine gene expression microarray dataset to be used with the GeneSpring GX 9/10 Data Analysis Tutorial for Agilent data.

Probe Summarization

RMA Probe Summarization This document contains all of the comparable features and options for RMA probe summarization and normalization in GeneSpring GX 7.3.1 and 9/10. It details the subtle differences in probe summarization and normalization using RMA for Affymetrix gene expression data, and also describe the steps involved in both versions.		GCRMA Probe Summarization This document contains all of the comparable features and options for GCRMA probe summarization and normalization in GeneSpring GX 7.3.1 and 9/10. It details the subtle differences in probe summarization and normalization using GCRMA for Affymetrix gene expression data, and also describe the steps involved in both versions.

R Scripts

R Script Technical Replicates This R script will enable you to perform T-Test against zero with Benjamini and Hochberg FDR in GeneSpring GX 10 when you have dye swapped technical replicates.

GeneSpring GX 7

Documentation

GeneSpring GX 7 Getting Quick Start Guide GeneSpring GX 7 User Manual GeneSpring GX 7 Getting Started Guide GeneSpring GX 7 Tutorials
External Programs and Databases

Connecting GeneSpring GX to Databases Learn to configure GeneSpring GX to connect directly to an Affymetrix GCOS database or a BASE MySQL database.		External Program Interface How do I link an external program to GeneSpring GX?

R-Integration Package The GeneSpring GX R-integration package will allow you to integrate R programs seamlessly into GeneSpring GX.		GeneSpring GX Affymetrix Plug-in The GeneSpring GX plug-ins allows GeneSpring GX to read Affymetrix CHP files and CEL files with RMA and GC-RMA normalization.

Resolver System - GeneSpring Connector Combine the power of the Rosetta Resolver System with GeneSpring GX.		GeneSpring-PathwayStudio Connector Integrate GeneSpring GX with the PathwayStudio tool of Adriadne Genomics.

GeneSpring GX and MetaCore Pathway Analysis Tool Integration The GeneSpring GX – MetaCore connector scripts will allow you to integrate GeneSpring GX version 7.3, and later, with the MetaCore pathway analysis tool.		GeneSpring GX and Ingenuity Pathways Analysis Integration The GeneSpring GX – IPA connector scripts will allow you to integrate GeneSpring GX with the Ingenuity Pathways Analysis tool.
Genomes

Genome Sequences Partial sequences for human, mouse and rat genomes that can be used in regulatory sequence searches - zip files and instructions.		GeneSpring GX Web Links Commonly used hypertext links to add during the genome installation.

Human NlaIII SAGE genome Download the Human NlaIII SAGE genome and guide to work with SAGE data in GeneSpring.
MIAME Compliance

Standard Attributes File A customizable XML file that can be used in GeneSpring GX or GeneSpring GX Workgroup to list all attributes that can be associated with a sample.
Pathways

GenMAPP Pathways Please note that GenMAPP pathways are included in the genomes available from within GeneSpring GX. To download a genome, open GeneSpring and select: File » Import Genome » Download a Standard Genome.		KEGG Pathways How do I get KEGG pathways into GeneSpring GX?
Physical Position View

Human Cytogenetic Band Zip file containing cytogenetic map locations for human chromosomes.		Mouse Cytogenetic Band Zip file containing cytogenetic map locations for mouse chromosomes.