Search PubMed⌕ Search

PubMed · 15531610

CGH-Explorer: a program for analysis of array-CGH data.

Abstract

SUMMARY: CGH-Explorer is a program for visualization and statistical analysis of microarray-based comparative genomic hybridization (array-CGH) data. The program has preprocessing facilities, tools for graphical exploration of individual arrays or groups of arrays, and tools for statistical identification of regions of amplification and deletion.

Explore related subjects

Keep this discovery

Explore connections, maps & timelines

BibTeXRIS

Ole Christian Lingjaerde, Lars O Baumbusch, Knut Liestøl, Ingrid K Glad, Anne-Lise Børresen-Dale. 2004-11-05. CGH-Explorer: a program for analysis of array-CGH data.. https://doi.org/10.1093/bioinformatics%2Fbti113

Cite the original work for its findings. Save a collection to share your selection of sources.

KEEP EXPLORING

Related citations

A software tool for 2D/3D visualization and analysis of phase-space data generated by Monte Carlo modelling of medical linear accelerators.

A computer program has been developed for novel 2D/3D visualization and analysis of the phase-space parameters of Monte Carlo simulations of medical accelerator radiation beams. The software is written in the IDL language and reads the phase-space data generated in the BEAMnrc/BEAM Monte Carlo code format. Contour and colour-wash plots of the fluence, mean energy, energy fluence, mean angle, spectra distribution, energy fluence distribution, angular distribution, and slices and projections of the 3D ZLAST distribution can be calculated and displayed. Based on our experience of using it at Massachusetts General Hospital, the software has proven to be a useful tool for analysis and verification of the Monte Carlo generated phase-space files. The software is in the public domain.

Computer Graphics↗

An extension of the transparent-motion detection limit using speed-tuned global-motion systems.

When transparent motion is defined purely by direction differences, no more than two signal directions can be detected simultaneously. This limit appears to occur because higher signal intensities are required to detect transparent motion compared with uni-directional motion (Edwards, M., & Greenwood, J. A. (2005). The perception of motion transparency: A signal-to-noise limit. Vision Research, 45, 1877-1884). Increasing the effective signal intensities should therefore increase the number of signals that can be detected. We achieved this by adding speed differences, dividing transparent-motion signals between two speed-tuned global-motion systems. When some signals moved at appropriate low speeds and others at high speeds, up to three signals were detected. This is consistent, at least in part, with the signal-to-noise processing basis of the transparency limit. Differences in contrast polarity were also used to assess whether the limit could be extended using stimulus features without independent global-motion systems. A modest improvement in performance was obtained, suggesting that there may be multiple routes to extending the transparent-motion limit.

Computer Graphics↗

A practical toolkit for computational steering.

Computational steering refers to the real-time interaction of a scientist with their running simulation code. Despite the many benefits associated with computational steering, its uptake to date has been limited. In this paper we discuss the reasons for this and how the computational steering library and associated tools developed as part of the RealityGrid project aim to tackle them. We describe the functionality of the steering library and the use of Grid services in constructing a generic, dynamic architecture for discovering, steering and connecting visualization software to running simulations. The use of on-line visualization for providing feedback to the scientist is described, including the ways in which it may be enhanced through tools such as Chromium and Access Grid. Finally, we illustrate the flexibility of our approach by describing the functionality that has been added to various simulation codes as part of the RealityGrid project.

Computer Graphics↗