rCGH 1.0.2 – Analyzing and Visualizing Agilent and Affymetrix Array-Based CGH Data

rCGH 1.0.2

:: DESCRIPTION

rCGH is a comprehensive array-based comparative genomic hybridization analysis workflow, integrating computational improvements and functionalities specifically designed for precision medicine.

aCGH_viewer – visualize aCGH profiles from uploaded segmentation tables.

::DEVELOPER

Frederic Commo <frederic.commo at gustaveroussy.fr>

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows/Mac OsX / Linux
  • R/ BioConductor

:: DOWNLOAD

 rCGHaCGH_viewer

:: MORE INFORMATION

Citation

rCGH: a comprehensive array-based genomic profile platform for precision medicine.
Commo F, Guinney J, Ferté C, Bot B, Lefebvre C, Soria JC, André F.
Bioinformatics. 2015 Dec 26. pii: btv718.

crlmm 1.28.0 – Genotype Calling and Copy Number Analysis tool for Affymetrix SNP 5.0 and 6.0 and Illumina arrays

crlmm 1.28.0

:: DESCRIPTION

The R package crlmm implements a multilevel model that adjusts for batch effects and provides allele-specific estimates of copy number.

::DEVELOPER

Division of Biostatistics and Bioinformatics – Johns Hopkins University Oncology

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux/ WIndows/ MacOsX
  • R
  • BioConductor

:: DOWNLOAD

 crlmm

:: MORE INFORMATION

Citation

J Stat Softw. 2011 May 1;40(12):1-32.
Using the R Package crlmm for Genotyping and Copy Number Estimation.
Scharpf RB1, Irizarry RA, Ritchie ME, Carvalho B, Ruczinski I.

HGNChelper 0.3.1 – Handy functions for working with HGNC Gene Symbols and Affymetrix probeset identifiers

HGNChelper 0.3.1

:: DESCRIPTION

HGNChelper contains functions for identifying and correcting HGNC gene symbols which have been converted to date format by Excel, for reversibly converting between HGNC symbols and valid R names, identifying invalid HGNC symbols and correcting synonyms and outdated symbols which can be mapped to an official symbol.

::DEVELOPER

Giovanni Parmigiani

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux/Windows/MacOsX
  • R package

:: DOWNLOAD

 HGNChelper

:: MORE INFORMATION

Starr 1.24.0 – Simple Tiling ARRay analysis of Affymetrix ChIP-chip data

Starr 1.24.0

:: DESCRIPTION

Starr is open-source R/Bioconductor package that facilitates comparative analysis of ChIP-chip data across experiments and across different microarray platforms.

::DEVELOPER

Tresch Group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows/Linux/MacOsX
  • R
  • BioConductor

:: DOWNLOAD

 Starr

:: MORE INFORMATION

Citation

Starr: Simple Tiling ARRay analysis of Affymetrix ChIP-chip data.
Zacher B, Kuan PF, Tresch A.
BMC Bioinformatics. 2010 Apr 17;11:194. doi: 10.1186/1471-2105-11-194.

affylmGUI 1.42.0 – Affymetrix linear modeling Graphical User Interface

affylmGUI 1.42.0

:: 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

affylmGUI

:: 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.

Mask / maskBAD 1.12.0 – Mask bad Probes in Affymetrix Expression data

Mask / maskBAD 1.12.0

:: 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.

Affyrmation 20140403 – Affirmation System for Affymetrix SNP Chip

Affyrmation 20140403

:: DESCRIPTION

Affyrmation is a marker affirmation system for Affymetrix SNP Chip.  This system performs real-time Affymetrix SNP Information Affirmation among NCBI, UCSC and SNPper websites, and supports batch processing by uploading a file.

::DEVELOPER

Affyrmation team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

Chen, Y.H., Tsai, M.F. and Yao, A. (2006)
Affyrmation: Online Real-time Affirmation and Annotation for Affymetrix SNP Information,
Journal of Genetics and Molecular Biology Vol. 17, No. 3, 156-161, September 1, 2006

IdeogramBrowser 0.20.4 – Visualization of Genomic Aberrations using Affymetrix SNP Arrays

IdeogramBrowser 0.20.4

:: DESCRIPTION

IdeogramBrowser  was specifically designed for use with the Affymetrix SNP arrays. It provides an interactive karyotypic visualization of multiple aberration profiles and direct links to GeneCards.

::DEVELOPER

Medical Systems Biology, University of Ulm

:: SCREENSHOTS

IdeogramBrowser

:: REQUIREMENTS

  • Windows/MacOsX/Linux
  • Java
:: DOWNLOAD

 IdeogramBrowser

:: MORE INFORMATION

Citation

André Müller, Karlheinz Holzmann and Hans A. Kestler
Visualization of genomic aberrations using Affymetrix SNP arrays
Bioinformatics (2007) 23 (4): 496-497.

Illumina2Affy v1/v2/v3 – Converts Illumina files into Affymetrix-style file.

Illumina2Affy v1/v2/v3

:: DESCRIPTION

Illumina2Affy converts Illumina files containing ONE/MULTIPLE individual’s genotype data of the format shown below into an Affymetrix-style file.

::DEVELOPER

Leeds Institute of Molecular Medicine

:: SCREENSHOTS

Illumina2Affy

:: REQUIREMENTS

  • Windows
  • Microsoft .NET framework version 2.0

:: DOWNLOAD

   Illumina2Affy

:: MORE INFORMATION

SNPannotator 20090828 – Adding Physical and Genetic Position data to Affymetrix Genotype files

SNPannotator 20090828

:: DESCRIPTION

SNPannotator is designed to annotate the text output files from Affymetrix SNP 6.0 chips. These files are no longer annotated by the Affymetrix console, and so cannot be used by the other programs listed here.

::DEVELOPER

Leeds Institute of Molecular Medicine

:: SCREENSHOTS

SNPannotator

:: REQUIREMENTS

  • Windows
  • Microsoft .NET framework version 2.0

:: DOWNLOAD

 SNPannotator

:: MORE INFORMATION