Software

From BioInfo

Supported and Installed Software:

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

[edit] Repositories

• The Core's GenoPub DAS2 (Distributed Annotation System) server
• The HCI's Supplemental Paper Info Repository
• GNomEx - the cores NextGen and Microarray LIMS and Analysis database.

[edit] Next Generation Sequencing

• Sequencing with our Illumina sequencers, recommendations
• USeq project analysis software, developed by the core for chIP-seq, RNA-seq, bis-seq, etc.
• Tomato - a framework for pipelines to analyze sequencing data in high performance clusters
• Hat - an application to do hi-sequencing analysis on local HCI-servers
• Solexa Pipeline - outline of requirements for supporting an Illumina sequencer

[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

[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] Utilities

• AgilentFilter - tool for filtering and reformatting Agilent microarray data files.
• CreateAnalysis - java app for creating a new analysis entry in GNomEx to deposit analysis files in a batch job.