Mask / maskBAD 1.36.0 – Mask bad Probes in Affymetrix Expression data

Mask / maskBAD 1.36.0

:: DESCRIPTION

Mask is an R package and contains several functions to handle Affymetrix expression data. Its goal is to mask BAD probes that bias the expression results.

::DEVELOPER

Michael Dannemann, Michael Lachmann @Department of Genetics/Bioinformatics – Max Planck Institut

:: SCREENSHOTS

N/A

:: REQUIREMENTS

:: DOWNLOAD

 Mask

:: MORE INFORMATION

Citation

BMC Bioinformatics. 2012 Apr 16;13:56. doi: 10.1186/1471-2105-13-56.
‘maskBAD’–a package to detect and remove Affymetrix probes with binding affinity differences.
Dannemann M, Lachmann M, Lorenc A.

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

:: 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.

PhyloTrack 2.1 – D3.js and JBrowse for Phylogeny and Positioning of Samples

PhyloTrack 2.1

:: DESCRIPTION

PhyloTrack is a JavaScript–based software tool that integrates the D3.js library for data visualization with the JBrowse tool for genome browser representation.

::DEVELOPER

PhyloTrack team

:: SCREENSHOTS

::REQUIREMENTS

  • Linux
  • Perl
  • JavaScript

:: DOWNLOAD

 PhyloTrack

:: MORE INFORMATION

Citation

PhyTB: Phylogenetic tree visualisation and sample positioning for M. tuberculosis.
Benavente ED, Coll F, Furnham N, McNerney R, Glynn JR, Campino S, Pain A, Mohareb FR, Clark TG.
BMC Bioinformatics. 2015 May 13;16:155. doi: 10.1186/s12859-015-0603-3.

BGX 1.58.0 – Bayesian integrated analysis of Affymetrix GeneChips

BGX 1.58.0

:: DESCRIPTION

BGX is a Bioconductor package for the Bayesian integrated analysis of Affymetrix GeneChips.

::DEVELOPER

BGX team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

:: DOWNLOAD

 BGX

:: MORE INFORMATION

Citation

BGX: a Bioconductor package for the Bayesian integrated analysis of Affymetrix GeneChips.
Turro E, Bochkina N, Hein AM, Richardson S.
BMC Bioinformatics. 2007 Nov 12;8:439.

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

ITALICS 2.52.0 – Normalize of Affymetrix GeneChip Human Mapping 100K and 500K set

ITALICS 2.52.0

:: DESCRIPTION

ITALICS (ITerative and Alternative normaLIzation and Copy number calling for affymetrix Snp arrays) is a normalization method that estimates both biological and non-relevant effects in an alternate, iterative manner, accurately eliminating irrelevant effects.

::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

ITALICS

:: MORE INFORMATION

Citation

Bioinformatics. 2008 Mar 15;24(6):768-74. doi: 10.1093/bioinformatics/btn048.
ITALICS: an algorithm for normalization and DNA copy number calling for Affymetrix SNP arrays.
Rigaill G, Hupé P, Almeida A, La Rosa P, Meyniel JP, Decraene C, Barillot E.

affylmGUI 1.66.0 – Affymetrix linear modeling Graphical User Interface

affylmGUI 1.66.0

:: DESCRIPTION

affylmGUI is a Graphical User Interface for analysis of Affymetrix microarray data, using the limma package (Linear Models for MicroArray data). affylmGUI is for Affymetrix data only.

::DEVELOPER

WEHI Bioinformatics

:: SCREENSHOTS

:: REQUIREMENTS

:: DOWNLOAD

 affylmGUI

:: MORE INFORMATION

Citation

affylmGUI: a graphical user interface for linear modeling of single channel microarray data.
Wettenhall JM, Simpson KM, Satterley K, Smyth GK.
Bioinformatics. 2006 Apr 1;22(7):897-9. Epub 2006 Feb 2.

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.

ALFALFA 0.8.1 – A Long Fragment Aligner

ALFALFA 0.8.1

:: DESCRIPTION

The long read mapper ALFALFA achieves high performance in accurately mapping long (>500bp) single-end and paired-end reads to gigabase-scale reference genomes, while remaining competitive for mapping shorter (>100bp) reads.

::DEVELOPER

ALFALFA team

:: SCREENSHOTS

N/A

::REQUIREMENTS

  • Linux

:: DOWNLOAD

 ALFALFA

:: MORE INFORMATION

Citation

A Long Fragment Aligner called ALFALFA.
Vyverman M, Baets B, Fack V, Dawyndt P.
BMC Bioinformatics. 2015 May 15;16(1):159.

Minfi 1.38.0 – Analyze Illumina’s 450k Methylation Arrays

Minfi 1.38.0

:: DESCRIPTION

Minfi is a flexible and comprehensive Bioconductor package for the analysis of Infinium DNA methylation microarrays.

::DEVELOPER

Hansen Lab

:: REQUIREMENTS

  • Linux / Windows/ MacOsX
  • R
  • BioCOnductor

:: DOWNLOAD

 Minfi

:: MORE INFORMATION

Citation

Bioinformatics. 2014 May 15;30(10):1363-9. doi: 10.1093/bioinformatics/btu049. Epub 2014 Jan 28.
Minfi: a flexible and comprehensive Bioconductor package for the analysis of Infinium DNA methylation microarrays.
Aryee MJ1, Jaffe AE, Corrada-Bravo H, Ladd-Acosta C, Feinberg AP, Hansen KD, Irizarry RA.