aroma.affymetrix 1.5.0
aroma.cn 0.4.4
What's new?
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, Submitted (2010-02-24)
URL: http://r-forge.r-project.org/R/?group_id=587
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/
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: http://groups.google.com/group/gadaproject
URL: http://groups.google.com/group/gadaproject/web/connection-with-aroma-affymetrix
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/
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.math.utu.fi/en/research/groups/bio/projects/peca.html
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