Tag: SNP Array

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.

FISH Oracle 2 – Visualize Data from multiple Array CGH or SNP Array Experiments

FISH Oracle 2

:: DESCRIPTION

FISH Oracle is a web-based software to visualize data from multiple array CGH or SNP array experiments in a genomic context. Its fast visualization engine and advanced web and database technology supports highly interactive use. FISH Oracle comes with a convenient data import mechanism, powerful search options for genomic elements (like gene names or karyobands), quick navigation and  zooming into interesting regions, and mechanisms to export the visualization into different high quality image formats (PDF, PS, PNG, SVG).

::DEVELOPER

RESEARCH GROUP FOR GENOME INFORMATICS ,Center for Bioinformatics, University of Hamburg

:: SCREENSHOTS

:: REQUIREMENTS

  • Linux / MacOsX
  • MySQL
  • Java
  • Apache Tomcat server
  • GenomeTools

:: DOWNLOAD

  FISH Oracle

:: MORE INFORMATION

Citation

M. Mader, R. Simon, S. Steinbiss and S. Kurtz:
FISH Oracle: a web server for flexible visualization of DNA copy number data in a genomic context.
Journal of Clinical Bioinformatics, 1:20 (2011)

SNPchip 2.14.0 – R Classes and methods for SNP Array data

SNPchip 2.14.0

:: DESCRIPTION

SNPchip defines methods for visualizing high-throughput genomic data

::DEVELOPER

Ingo Ruczinski

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux/ WIndows/ MacOsX
  • R
  • BioConductor

:: DOWNLOAD

 SNPchip

:: MORE INFORMATION

Citation

Bioinformatics. 2007 Mar 1;23(5):627-8. Epub 2007 Jan 4.
SNPchip: R classes and methods for SNP array data.
Scharpf RB1, Ting JC, Pevsner J, Ruczinski I.

Rseg 1.0 – an R package to Optimize Segmentation of SNP array data

Rseg 1.0

:: DESCRIPTION

Rseg allows the user to define sample-specific thresholds to call gains and losses in an interactive way. It also allows the user to correct for RMA induced normalization artifacts in case of imbalance between losses and gains.

::DEVELOPER

Lamy P (plamy@cs.au.dk), Wiuf C, Ørntoft TF, Andersen CL.

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows/ Linux / MacOsX
  • R package

:: DOWNLOAD

 Rseg

:: MORE INFORMATION

Citation

Rseg–an R package to optimize segmentation of SNP array data.
Lamy P, Wiuf C, Ørntoft TF, Andersen CL.
Bioinformatics. 2011 Feb 1;27(3):419-20.

SAQC 1.0 – SNP Array Quality Control

SAQC 1.0

:: DESCRIPTION

SAQC (SNP Array Quality Control)software is written in R and R-GUI and was developed as a user-friendly tool for the visualization and evaluation of data quality of genome-wide SNP arrays.

::DEVELOPER

Hsin-Chou Yang

:: SCREENSHOTS

::REQUIREMENTS

:: DOWNLOAD

 SAQC

:: MORE INFORMATION

Citation

Hsin-Chou Yang*, Hsin-Chi Lin, Meijyh Kang, Chun-Houh Chen, Chien-Wei Lin, Ling-Hui Li, Jer-Yuarn Wu, Yuan-Tsong Chen, and Wen-Harn Pan (2011).
SAQC: SNP array quality control.
BMC Bioinformatics 12, 100.

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