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: https://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: https://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: https://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: https://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: https://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: https://www.progenetix.net//
URL: https://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/