RRC-CGF: Data Analysis Tools

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Affymetrix Expression Console Software
http://www.affymetrix.com/estore/browse/level_seven_software_products_only.jsp?productId=131414#1_1
This software enables the visualization of microarray QC metrics and the generation of CHP files from CEL files with minimal effort using standardized approaches tailored by Affymetrix. Alternatively, more advanced users can configure the background correction, normalization, and summarization methods to meet the needs of their experimental research.
Affymetrix Transcriptome Analysis Console 2.0 Software
http://www.affymetrix.com/estore/browse/level_seven_software_products_only.jsp?productId=prod760001&categoryId=35623&productName=Transcriptome-Analysis-Console#1_1
Transcriptome Analysis Console 2.0 Software, developed by Affymetrix, enables the identification of differentially expressed genes and exons and the visualization of alternative splicing events for determining possible transcript isoforms that may exist in your specific samples.
Affymetrix Chromosome Analysis Suite (ChAS) Software
http://www.affymetrix.com/catalog/131408/AFFY/Chromosome+Analysis+Suite+%28ChAS%29+Software#1_1
This software performs various types of analysis on Affymetrix copy number and cytogenetics files.
The R Project for Statistical Computing
http://www.r-project.org/
Excerpt — “R is a free software environment for statistical computing and graphics. It compiles and runs on a wide variety of UNIX platforms, Windows and MacOS.”
Bioconductor
http://www.bioconductor.org/
A cross-platform, open-source genomic data analysis and comprehension software.
Cytoscape
http://cytoscape.org/
A cross-platform, open-source bioinformatics platform for visualizing and integrating molecular interaction networks.
Osprey
http://biodata.mshri.on.ca/osprey/
A cross-platform, software from Mount Sinai Hospital in Toronto, Canada for visualizing interaction networks
dChip (DNA-chip analyzer)
http://www.biostat.harvard.edu/complab/dchip/
dChip Software: Analysis and visualization of gene expression and SNP microarrays
Database for Annotation, Visualization and Integrated Discovery (DAVID)
http://david.abcc.ncifcrf.gov/
Excerpt — “DAVID [...] provides a comprehensive set of functional annotation tools for investigators to understand biological meaning behind large list of genes.”
PAM: Prediction Analysis for Microarrays
http://www-stat.stanford.edu/~tibs/PAM/
SAM Significant Analysis of Microarrays
http://www-stat.stanford.edu/~tibs/SAM/
SNOMAD - Standardization and NOrmalization of MicroArray Data
http://pevsnerlab.kennedykrieger.org/snomadinput.html
Web-based gene expression data analysis tools.
Gene Set Enrichment Analysis (GSEA)
http://www.broadinstitute.org/gsea/
Excerpt — “[...] a computational method that determines whether an a priori defined set of genes shows statistically significant, concordant differences between two biological states (e.g. phenotypes).”


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