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Add ons

Addons to the Aroma Framework

Add on: ACNE

Title: ACNE - Affymetrix SNP probe-summarization using non-negative matrix factorization
Authors: Maria Ortiz-Estevez, Angel Rubio, Henrik Bengtsson
Description: Package for NMF summarization of SNP probes.
Chip types: All Affymetrix genotyping and CN arrays.
Requirements: Cross platform, aroma.affymetrix
References: M. Ortiz-Estevez, H. Bengtsson, A. Rubio, ACNE: a summarization method to estimate allele-specific copy numbers for Affymetrix SNP arrays, Bioinformatics, 2010.
URL: http://r-forge.r-project.org/R/?group_id=587

Add on: CalMaTe

Title: CalMaTe - A post-calibration process to improve allele-specific copy number estimates from SNP microarrays
Authors: Maria Ortiz-Estevez, Ander Aramburu, Henrik Bengtsson, Pierre Neuvial, Angel Rubio.
Description: Package for calibrating allele-specific copy number estimates (ASCNs).
Chip types: Any genotyping and CN arrays, e.g. Affymetrix and Illumina.
Requirements: Cross platform, aroma.core
References: Ortiz-Estevez et al., CalMaTe: A method and software to improve allele-specific copy number of SNP arrays for downstream segmentation, Bioinformatics, 2012.
URL: http://r-forge.r-project.org/R/?group_id=587

Add on: FIRMAGene

Title: FIRMAGene - differential splicing for Affymetrix Gene 1.0 ST
Authors: Mark Robinson
Description:
Chip types: Affymetrix Gene 1.0 ST
Requirements: Cross platform, aroma.affymetrix
References: M. Robinson and TS. Speed, Differential splicing using whole-transcript microarrays, BMC Bioinformatics, 2009.
URL: http://r-forge.r-project.org/R/?group_id=424
URL: http://bioinf.wehi.edu.au/folders/firmagene/

Add on: GADA (Genome Alteration Detection Analysis)

Authors: Pique-Regi et al.
Description: "GADA is a fast and accurate method for detecting copy number alterations (CNA) from array data. [...]"
Chip types: Generic segmentation method applicable to all raw CNs.
Operating system: ?
References: (1) Pique-Regi R and Gonzalez JR: "R-Gada: a package for fast and parallel detection of copy number on multiple samples and visualization", Bioinformatics, Submitted Dec 2008, (2) Pique-Regi R, Monso-Varona J,Ortega A, Seeger RC, Triche TJ, Asgharzadeh S: "Sparse representation and Bayesian detection of the genome copy number alterations from microarray data", Bioinformatics, Feb 2008
URL: https://r-forge.r-project.org/R/?group_id=915
URL: http://groups.google.com/group/gadaproject
URL: http://biron.usc.edu/~piquereg/GADA/

Other tools leveraging aroma.* packages

AMDA

Authors: Genopolis
Operating system: Cross platform
Description: Automated Microarray Data Analysis (AMDA) software
References:
URL: http://www.genopolis.it/

BRB-ArrayTools

Authors: Richard Simon & BRB-ArrayTools Development Team
Operating system: Windows with MS Excel
Description: "BRB-ArrayTools is an integrated package for the visualization and statistical analysis of DNA microarray gene expression data. It was developed by professional statisticians experienced in the analysis of microarray data and involved in the development of improved methods for the design and analysis of microarray based experiments. The array tools package utilizes an Excel front end. Scientists are familiar with Excel and utilizing Excel as the front end makes the system portable and not tied to any database. [...]"
References:
URL: http://linus.nci.nih.gov/BRB-ArrayTools.html

Expander

Authors: Ron Shamir's Computational Genomics Laboratory, School of Computer Science, Tel Aviv University
Operating system: Java
Description: "EXPANDER (EXpression Analyzer and DisplayER) is a java-based tool for analysis of gene expression data. It is capable of (1) clustering (2) visualizing (3) biclustering and (4) performing downstream analysis of clusters and biclusters such as functional enrichment and promoter analysis. In particular, it can analyze groups of genes for enrichment of transcription factor binding sites in their promoters."
References:
URL: http://acgt.cs.tau.ac.il/expander/

O-miner

Authors: Cutts et al, Molecular Oncology, Barts Cancer Institute, Queen Mary's School of Medicine and Dentistry, UK.
Operating system: Online Server
Description: "O-miner is a project designed to automate the analysis and annotation of complex -omics data. The software is easy to use and freely available to the scientific community. Users can upload data via a web page and can be notified by email when their analysis is completed. The output includes detailed data analysis reports and diagrams. [As of May 2012] genomics and transcriptomics analysis options are available".
References: RJ Cutts et al. O-miner: an integrative platform for automated analysis and mining of -omics data, NAR 2012.
URL: http://o-miner.org/

PECA (Probe-level expression change averaging)

Authors: Laura L. Elo, Jukka Hiissa
Description: The PECA R-package implements the Probe-level Expression Change Averaging (PECA) procedure for the identification of differentially expressed genes or differentially spliced exons in Affymetrix gene or exon microarray studies.
References:
URL: http://www.utu.fi/en/units/sci/units/math/Research/biomathematics/projects/Pages/peca.aspx

Progenetix / tastyAroma

Authors: M Baudis
Description: "tastyAroma is a project for providing interfaces and standard procedures as well as advanced plotting functions to the aroma.affymetrix array analysis packages. ... Additionally, the tastyAroma project provides scripts for the integration of analysis results into a web portal, relying on libraries of the Progenetix project.
References:
URL: http://www.progenetix.net/
URL: http://www.progenetix.net/progenetixWiki/pmwiki.php/TastyAroma/TastyAroma

Repitools

Authors: A. Statham et al.
Description: "Useful functions for quality assessment, visualization, summarization and statistical analysis of epigenomics experiments."
References: A. Statham et al., Repitools: an R package for the analysis of enrichment-based epigenomic data, Bioinformatics, 2010.
URL: http://repitools.r-forge.r-project.org/