Tag: Microarray

metaArray 1.66.0 – Integration of Microarray Data for Meta-analysis

metaArray 1.66.0

:: DESCRIPTION

metaArray is a general probabilistic framework for combining high-throughput genomic data from several related microarray experiments using mixture models.

::DEVELOPER

metaArray team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux/MacOsX/ WIndows
  • R package
  • BioCOnductor

:: DOWNLOAD

  metaArray

:: MORE INFORMATION

Citation:

BMC Bioinformatics. 2007 Sep 27;8:364.
A latent variable approach for meta-analysis of gene expression data from multiple microarray experiments.
Choi H1, Shen R, Chinnaiyan AM, Ghosh D.

limmaGUI 1.68.0 – Linear Models for Microarrays Graphical User Interface

limmaGUI 1.68.0

:: DESCRIPTION

limmaGUI is a Graphical User Interface for Gordon Smyth’s limma package (Linear Models for MicroArray data). It uses state-of-the-art statistical techniques to normalize microarray data, perform diagnostic plots and to find differentially expressed genes in complex experimental designs.

::DEVELOPER

WEHI Bioinformatics

:: SCREENSHOTS

limmaGUI

:: REQUIREMENTS

:: DOWNLOAD

 limmaGUI

:: MORE INFORMATION

Citation

Bioinformatics. 2004 Dec 12;20(18):3705-6. Epub 2004 Aug 5.
limmaGUI: a graphical user interface for linear modeling of microarray data.
Wettenhall JM, Smyth GK.

illuminaio 0.34.0 – Parsing Illumina Microarray Output Files

illuminaio 0.34.0

:: DESCRIPTION

illuminaio is a suit of tools for parsing Illuminas microarray output files, including IDAT.

::DEVELOPER

Hansen Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Windows/ MacOsX
  • R
  • BioCOnductor

:: DOWNLOAD

 illuminaio

:: MORE INFORMATION

Citation

F1000Res. 2013 Dec 4;2:264. doi: 10.12688/f1000research.2-264.v1. eCollection 2013.
illuminaio: An open source IDAT parsing tool for Illumina microarrays.
Smith ML, Baggerly KA, Bengtsson H, Ritchie ME, Hansen KD

MANOR 1.64.0 – Micro-Array NORmalization of array-CGH data

MANOR 1.64.0

:: DESCRIPTION

MANOR (Micro-Array NORmalization) is a software which is devoted to the normalization of Array Comparative Genomic Hybridization (array-CGH) data.

::DEVELOPER

U900 Institut Curie – INSERM/Mines ParisTech “Bioinformatics and Computational Systems Biology of Cancer

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux/ Windows/ MacOsX
  • R package
  • Bioconductor

:: DOWNLOAD

 MANOR

:: MORE INFORMATION

Citation

BMC Bioinformatics. 2006 May 22;7:264.
Spatial normalization of array-CGH data.
Neuvial P, Hupé P, Brito I, Liva S, Manié E, Brennetot C, Radvanyi F, Aurias A, Barillot E.

massiR 1.28.0 – MicroArray Sample Sex Identifier

massiR 1.28.0

:: DESCRIPTION

massiR package provides a method for researchers to predict the sex of samples in microarray datasets.

::DEVELOPER

Sam Buckberry <sam.buckberry at adelaide.edu.au>

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Windows/ MacOsX
  • R
  • BioConductor

:: DOWNLOAD

 massiR

:: MORE INFORMATION

Citation

Bioinformatics. 2014 Apr 16.
massiR: a method for predicting the sex of samples in gene expression microarray datasets.
Buckberry S1, Bent SJ, Bianco-Miotto T, Roberts CT.

TurboNorm 1.40.0 – A fast Scatterplot Smoother Suitable for Microarray Normalization

TurboNorm 1.40.0

:: DESCRIPTION

TurboNorm is a software for fast scatterplot smoother based on B-splines with second-order difference penalty.

::DEVELOPER

TurboNorm team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows/Linux/MacOsX
  • R
  • BioConductor

:: DOWNLOAD

 TurboNorm

:: MORE INFORMATION

Citation

Stat Appl Genet Mol Biol. 2012 Jul 12;11(4). pii: /j/sagmb.2012.11.issue-4/1544-6115.1753/1544-6115.1753.xml. doi: 10.1515/1544-6115.1753.
A novel and fast normalization method for high-density arrays.
van Iterson M, Duijkers FA, Meijerink JP, Admiraal P, van Ommen GJ, Boer JM, van Noesel MM, Menezes RX.

BASE 3.18.2 – Microarray Data Management & Analysis

BASE 3.18.2

:: DESCRIPTION

BASE (BioArray Software Environment) is a comprehensive free web-based database solution for the massive amounts of data generated by microarray analysis.

::DEVELOPER

Jari Häkkinen @ Lund University

:: SCREENSHOTS

:: REQUIREMENTS

:: DOWNLOAD

BASE

:: MORE INFORMATION

Citation:

Johan Vallon-Christersson, Nicklas Nordborg, Martin Svensson and Jari Häkkinen  ,
BASE – 2nd generation software for microarray data management and analysis
BMC Bioinformatics 2009, 10:33

maPredictDSC 1.30.0 – Ouctome Prediction using Microarray data

maPredictDSC 1.30.0

:: DESCRIPTION

maPredictDSC is a standard Bioconductor style R package meant to assist in developing prediction models from raw microarray data.

::DEVELOPER

the Bioinformatics and Computational Biology Unit of the Perinatology Research Branch (NICHD)

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows / Linux / MacOS
  • R package
  • Bioconductor

:: DOWNLOAD

 maPredictDSC

:: MORE INFORMATION

Citation

Bioinformatics. 2013 Nov 15;29(22):2892-9. doi: 10.1093/bioinformatics/btt492. Epub 2013 Aug 20.
Strengths and limitations of microarray-based phenotype prediction: lessons learned from the IMPROVER Diagnostic Signature Challenge.
Tarca AL1, Lauria M, Unger M, Bilal E, Boue S, Kumar Dey K, Hoeng J, Koeppl H, Martin F, Meyer P, Nandy P, Norel R, Peitsch M, Rice JJ, Romero R, Stolovitzky G, Talikka M, Xiang Y, Zechner C; IMPROVER DSC Collaborators.

AffyRNADegradation 1.38.0 – Analyze and Correct Probe Positional Bias in Microarray data due to RNA Degradation

AffyRNADegradation 1.38.0

:: DESCRIPTION

AffyRNADegradation helps with the assessment and correction of RNA degradation effects in Affymetrix 3′ expression arrays.

::DEVELOPER

Mario Fasold <fasold at izbi.uni-leipzig.de>

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux /  MacOsX / Window
  • R
  • BioConductor

:: DOWNLOAD

 AffyRNADegradation

:: MORE INFORMATION

Citation

Bioinformatics. 2013 Jan 1;29(1):129-31. doi: 10.1093/bioinformatics/bts629. Epub 2012 Oct 24.
AffyRNADegradation: control and correction of RNA quality effects in GeneChip expression data.
Fasold M1, Binder H.

Primegens 2.0.5 – Primer Design for Microarray

Primegens 2.0.5

:: DESCRIPTION

Primegens ((PRIMEr Design Using GEN Specific Fragments) is a software for high-throughput primer and probe design. The program uses two third party executables like Primer3 and Megablast.

::DEVELOPER

Primegens Team

:: SCREENSHOTS

:: REQUIREMENTS

  • Linux/Windows

:: DOWNLOAD

 Primegens

:: MORE INFORMATION

Citation

Gyan Prakash Srivastava, Juyuan Guo, Huidong Shi and Dong Xu.
” PRIMEGENS-v2: genome-wide primer design for analyzing DNA methylation pattern of CpG island“.
Bioinformatics 2008 24(17):1837-42.