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)

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.

smoothseg 0.0.4 – Robust smooth segmentation approach for array CGH data analysis

smoothseg 0.0.4

:: DESCRIPTION

smoothseg is an R package to compute smooth-segmentation of array CGH data, including the estimation of FDR for comparative studies.

::DEVELOPER

Huang Jian <j.huang@ucc.ie>,  Prof. Yudi Pawitan ,Arief Gusnanto <Arief.Gusnanto@mrc-bsu.cam.ac.uk>

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows/Linux /MacOsX
  • R package

:: DOWNLOAD

 smoothseg

:: MORE INFORMATION

Citation

Bioinformatics. 2007 Sep 15;23(18):2463-9. Epub 2007 Jul 27.
Robust smooth segmentation approach for array CGH data analysis.
Huang J1, Gusnanto A, O’Sullivan K, Staaf J, Borg A, Pawitan Y.

SLR 0.1.9 – Performing Smoothed Logistic Regression for CGH data

SLR 0.1.9

:: DESCRIPTION

SLR is a software of fitting smoothed logistic regression with Cauchy-Normal Random Probes Effects with application to aCGH data

::DEVELOPER

Huang Jian <j.huang@ucc.ie> Prof. Yudi Pawitan

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows/Linux /MacOsX
  • R package

:: DOWNLOAD

 SLR

:: MORE INFORMATION

Citation

Stat Med. 2009 Dec 30;28(30):3798-810. doi: 10.1002/sim.3753.
Classification of array CGH data using smoothed logistic regression model.
Huang J1, Salim A, Lei K, O’Sullivan K, Pawitan Y.

cghseg 1.0.2 – Segmentation Methods for Array CGH analysis

cghseg 1.0.2

:: DESCRIPTION

cghseg is an R package dedicated to the analysis of CGH profiles using segmentation models.

::DEVELOPER

cghseg team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows / Linux / MacOsX
  • R package
  • Bioconductor

:: DOWNLOAD

  cghseg

:: MORE INFORMATION

Citation

Biostatistics. 2011 Jul;12(3):413-28. doi: 10.1093/biostatistics/kxq076.
Joint segmentation, calling, and normalization of multiple CGH profiles.
Picard F, Lebarbier E, Hoebeke M, Rigaill G, Thiam B, Robin S.

CNVDetector 1.1 – Locate Copy Number Variations using Array CGH data

CNVDetector 1.1

:: DESCRIPTION

CNVDetector is a program for locating copy number variations in a single genome using array CGH data. This program can detect the aberration regions in the array CGH data and output as a tabbing file.

::DEVELOPER

Kun-Mao Chao

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows

:: DOWNLOAD

  CNVDetector

:: MORE INFORMATION

Citation

Chen, P.-A., Liu, H.-F., Chao, K.-M., 2008,
CNVDetector: Locating Copy Number Variations Using Array CGH Data“,
Bioinformatics, 24: 2773-2775.

 

SnoopCGH Beta – Visualise and Explore Comparative Genomic Hybridization (CGH) data

SnoopCGH Beta

:: DESCRIPTION

SnoopCGH is a java desktop application for visualising and exploring comparative genomic hybridization (CGH) data. The software allows the user to interactively analyse several sets of data simultaneously. The input is based on a tab-, space- or comma-delimited format, containing series of log intensity values corresponding to one or more comparisons or samples.

::DEVELOPER

Jacob Almagro-Garcia

:: SCREENSHOTS

:: REQUIREMENTS

  • Linux/windows /MacOsX
  • Java

:: DOWNLOAD

  SnoopCGH

:: MORE INFORMATION

Citation

Bioinformatics. 2009 Oct 15;25(20):2732-3. Epub 2009 Aug 16.
SnoopCGH: software for visualizing comparative genomic hybridization data.
Almagro-Garcia J, Manske M, Carret C, Campino S, Auburn S, Macinnis BL, Maslen G, Pain A, Newbold CI, Kwiatkowski DP, Clark TG.

 

CGH-Plotter 20051025 – MATLAB Toolbox for CGH-data Analysis

CGH-Plotter 20051025

:: DESCRIPTION

CGH-Plotter is a MATLAB toolbox with a graphical user interface for comparative genomic hybridization (CGH) data analysis. The CGH-Plotter identifies putative groups of genes whose copy-number is deleted or amplified using k-means clustering and dynamic programming. The CGH-Plotter allows also representative illustrations of CGH-data.

::DEVELOPER

Reija Autio, Sampsa Hautaniemi and Matti Saarela at Computational Systems Biology Research group

:: SCREENSHOTS

:: REQUIREMENTS

:: DOWNLOAD

CGH-Plotter

:: MORE INFORMATION

Citation:

Autio R, Hautaniemi S, Kauraniemi P, Yli-Harja O, Astola J, Wolf M, Kallioniemi A.
CGH-Plotter: MATLAB toolbox for CGH-data analysis.
Bioinformatics. 2003 Sep 1;19(13):1714-5.

Ginkgo 1.01 – CGH & Expression Microarray Data Analysis & Normalization

Ginkgo 1.01

:: DESCRIPTION

Ginkgo is a spotted microarray data pre-processing platform featuring analysis functionalities for CGH (Comparative Genomic Hybridization) and expression data. This application provides a user-friendly graphical interface that allows viewing, analyzing, generating and reporting microarray data, easily and intuitively. Within the software there are a number of algorithms to address microarray data analysis needs, including normalization, filtering, data imputation, replicates merge, and expression statistical distribution tests.

::DEVELOPER

J. Craig Venter Institute

:: SCREENSHOTS

:: REQUIREMENTS

  • Linux / Windows
  • JAVA

:: DOWNLOAD

Ginkgo

:: MORE INFORMATION

This application is released under the GPL v3 License: View License

Citation:

Quackenbush, J. Microarray data normalization and transformation. Nature Genetics. Vol.32 supplement pp496-501 (2002).