Software

From BioInfo

Supported and Installed Software:

Contents 1 Repositories 2 Databases 3 Genome Browsers 4 Gene Expression 5 Tiling 6 Next Generation Sequencers 7 Utilities

[edit] Repositories

• The Core's SVN Software Code repository
• The Core's DAS2 (Distributed Annotation System) server
• The HCI's Supplemental Paper Info Repository

[edit] Databases

• GNomEx - the core's new and improved raw results microaray database.
• CGAR - the core's genomic analysis repository, under construction.

[edit] Genome Browsers

• IGB - a highly sophisticated, cross platform, stand alone genome browser designed for real time visualization and manipulation of large genomic datasets. IGB has been adopted by the Core for genomic analysis.

• UCSC GB - a well supported web genome browser, complex organism centric

• Ensembl GB - a well supported web genome browser from across the pond

[edit] Gene Expression

• Bioconductor - Microarray analysis software library written in R, contributed by a variety of labs. Includes Rank Product (RankProd) analysis, Affymetrix (Affy) normalization package.

• R - Statistics programming language - needed for Bioconductor.

• GeneSpringGX - Commercial gene expression analysis program from Agilent.

• GeneSifter - Web-based commercial analysis tool. Combines statistical analysis tools with clustering, KEGG pathway, and Gene Ontology analysis methods. Contact the Microarray Bioinformatics Core for access.

• Spotfire DecisionSite - a commercial data visualization and analysis tool that is well suited to microarray data analysis. It has optional Functional Genomics and Statistics features that are useful for microarray data normalization and analysis. Spotfire is available on the Windows platform only.

• MeV from TM4 - a public domain analysis program that combines a wide variety of analysis tools including clustering, classification, and statistical analysis methods. It runs under MacOS, Windows, and Linux operating systems, and can be used for analysis of expression data from Agilent, Affymetrix, and spotted cDNA arrays.

• SAM - (Significance Analysis of Microarrays) is a statistical method for microarray data analysis. Stanford University distributes a Microsoft Excel add-in that performs SAM within an Excel spreadsheet. An excellent implementation of SAM is also available within MeV.

• PAM - (Prediction Analysis for Microarrays) is a sample classification method which uses the "nearest shrunken centroid" method. PAM builds a classifier based on a training data set, which can then classify unknown samples. Implemented in R.

[edit] Tiling

• Tiling Microarray Analysis Tools (a.k.a. T2, TiMAT2) - Command line software for processing and analyzing tiling microarray experiments.

• Agilent ChIP Analytics - for ChIP-chip experiments

• Agilent CGH Analytics - performs a variety quality control and aberration detection analyses on CGH arrays.

• MeV from TM4can perform some CGH analyses as well as gene expression analysis.

[edit] Next Generation Sequencers

• Sequencing with our Solexa, recommendations
• USeq project analysis software, developed by the core
• Solexa Pipeline - outline of requirements for supporting a Solexa signature sequencer

[edit] Utilities

• AgilentFilter - tool for filtering and reformatting Agilent microarray data files.