PUMA 3.26.0 – Propagating Uncertainty in Microarray Analysis

PUMA 3.26.0

:: DESCRIPTION

puma is a Bioconductor package incorporating a suite of analysis methods for use on Affymetrix GeneChip data.

:: DEVELOPER

BIOINFORMATICS @ MANCHESTER

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / windows/ MacOsX
  • BioConductor
  • R package

:: DOWNLOAD

 PUMA

:: MORE INFORMATION

Citation

puma: a Bioconductor package for propagating uncertainty in microarray analysis.
Pearson RD, Liu X, Sanguinetti G, Milo M, Lawrence ND, Rattray M.
BMC Bioinformatics. 2009 Jul 9;10:211. doi: 10.1186/1471-2105-10-211.

puma 3.0: improved uncertainty propagation methods for gene and transcript expression analysis.
Liu X, Gao Z, Zhang L, Rattray M.
BMC Bioinformatics. 2013 Feb 5;14:39. doi: 10.1186/1471-2105-14-39

R/maanova 1.54.0 – Environment for Microarray Analysis

R/maanova 1.54.0

:: DESCRIPTION

R/maanova (MicroArray ANalysis Of VAriance) is an extensible, interactive environment for Microarray analysis.

::DEVELOPER

The Churchill Group

:: SCREENSHOTS

:: REQUIREMENTS

  • Linux / Windows/ MacOsX
  •  / Java / MatLab

:: DOWNLOAD

 R/maanova

:: MORE INFORMATION

Citation

J Comput Biol. 2000;7(6):819-37.
Analysis of variance for gene expression microarray data.
Kerr MK1, Martin M, Churchill GA.

compdiagTools 1.8.8 – A Toolbox for Microarray Analysis

compdiagTools 1.8.8

:: DESCRIPTION

compdiagTools is an R package containing tools for analysis and illustration of microarray experiments.

::DEVELOPER

Institute of Functional Genomics

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows/Linux / MacOsX
  • R

:: DOWNLOAD

 compdiagTools

:: MORE INFORMATION

Citation

A toolbox for performing and illustrating microarray data analyses – user’s guide to the R package compdiagTools
Scheid S, Jäger J and Lottaz C
CompDiag Technical Report Nr. 2005/01 Mar. 2005

aroma.affymetrix 2.13.2 – Open-source R framework for your Microarray Analysis

aroma.affymetrix 2.13.2

:: DESCRIPTION

Aroma.affymetrix is an R package for analyzing large Affymetrix data sets.  It allows you to analyze 100-1,000s of arrays of various chip types, e.g. expression arrays, SNP chips, exon arrays and so on.

::DEVELOPER

Henrik Bengtsson et al. 

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux/MacOsX/Windows
  • R package

:: DOWNLOAD

 aroma.affymetrix

:: MORE INFORMATION

Citation

ACNE: a summarization method to estimate allele-specific copy numbers for Affymetrix SNP arrays.
Ortiz-Estevez M, Bengtsson H, Rubio A.
Bioinformatics. 2010 Aug 1;26(15):1827-33. doi: 10.1093/bioinformatics/btq300

Estimation and assessment of raw copy numbers at the single locus level.
Bengtsson H, Irizarry R, Carvalho B, Speed TP.
Bioinformatics. 2008 Mar 15;24(6):759-67. doi: 10.1093/bioinformatics/btn016.

VennMaster 0.38.2 – Venn Diagram Drawing tool for MicroArray Analysis

VennMaster 0.38.2

:: DESCRIPTION

VennMaster is a tool for drawing area proportional Venn/Euler-diagrams by importing gene lists from GoMiner.

::DEVELOPER

Medical Systems Biology, University of Ulm

:: SCREENSHOTS

:: REQUIREMENTS

  • Linux / Windows /MacOsX
  • Java

:: DOWNLOAD

 VennMaster

:: MORE INFORMATION

Citation

Hans A Kestler et al.
VennMaster: Area-proportional Euler diagrams for functional GO analysis of microarrays
BMC Bioinformatics 2008, 9:67

R functions for cDNA array analysis – cDNA Microarray Analysis

R functions for cDNA array analysis

:: DESCRIPTION

R functions for cDNA array analysis is a set of R functions for filtering, normalization, Bayesian hierarchical modelling and MCMC procedures in cDNA microarray analysis.

::DEVELOPER

George C. Tseng 

:: SCREENSHOTS

N/A

:: REQUIREMENTS

:: DOWNLOAD

  R functions for cDNA array analysis

:: MORE INFORMATION

Citation

George C. Tseng, Min-Kyu Oh, Lars Rohlin, James C. Liao, Wing Hung Wong (2001)
Issues in cDNA microarray analysis: quality filtering, channel normalization, models of variations and assessment of gene effects,
Nucleic Acids Res v29 p2549

SVDMAN 0.9b – Singular Value Decomposition Microarray ANalysis

SVDMAN 0.9b

:: DESCRIPTION

SVDMAN is a program for singular value decomposition analysis of global gene expression data. It is designed to operate both as a stand-alone command line executable and as a component of larger systems for gene expression analysis.

::DEVELOPER

Michael Wall

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows/Linux
  • C Compiler

:: DOWNLOAD

 SVDMAN

:: MORE INFORMATION

Citation

ME Wall, PA Dyck, TS Brettin.
SVDMAN — Singular value decomposition analysis of microarray data. 2001.
Bioinformatics 17:566-568.

MARS 1.2.0 – Microarray Analysis and Retrieval System

MARS 1.2.0

:: DESCRIPTION

 MARS (Microarray Analysis and Retrieval System) provides a comprehensive MIAME supportive suite for storing, retrieving, and analyzing multi color microarray data. The system comprises a lab notebook, a laboratory information management system (LIMS), a quality control management, as well as a sophisticated user management system. MARS is fully integrated into an analytical pipeline of microarray image analysis, normalization, gene expression clustering, and mapping of gene expression data onto biological pathways.

::DEVELOPER

Genomics & Bioinformatics Graz, Graz University of Technology

:: SCREENSHOTS

:: REQUIREMENTS

  • Linux / Windows / MacOsX
  • Java
  • Oracle / PostgreSQL / MySQL

:: DOWNLOAD

  MARS

:: MORE INFORMATION

Citation

Maurer M, Molidor R, Sturn A, Hartler J, Hackl H, Stocker G, Prokesch A, Scheideler M, Trajanoski Z.
MARS: microarray analysis, retrieval, and storage system.
BMC Bioinformatics. 6: 101-101 (2005)

F-SCAN 1.3 – Fluorescently Probed cDNA Microarray Analysis

F-SCAN 1.3

:: DESCRIPTION

F-SCAN is a software of Fluorescently Probed cDNA Microarray Analysis

::DEVELOPER

Analytical Biostatistics Section,NIH

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Windows / MacOsX
  • Matlab

:: DOWNLOAD

 F-SCAN

:: MORE INFORMATION

Citation:

A. J. Carlisle, V. V. Prabhu, A. Elkahloun, J. Hudson, J. M. Trent, W. M. Linehan, E. D. Williams, M. R. Emmert-Buck, L. A. Liotta, P. J. Munson, and D. B. Krizman;
Development of a Prostate cDNA Microarray and Statistical Gene Expression Analysis Package“;
Molecular Carcinogenesis 28:12-22 (2000)

SMA 0.5.13 – Statistics for Microarray Analysis

SMA 0.5.13

:: DESCRIPTION

SMA (Statistics for Microarray Analysis) is a collection of simple R functions that were used in the Microarray Analysis.

::DEVELOPER

Speed Berkeley Research group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

:: DOWNLOAD

 SMA

:: MORE INFORMATION

Citation:

Sandrine Dudoit, Yee Hwa Yang, Matt Callow and Terry Speed
Statistical methods for identifying differentially expressed genes in replicated cDNA microarray experiments.