CGHnormaliter: a Bioconductor package for normalization of array CGH data with many CNAs

Bart P P van Houte; Thomas W Binsl; Hannes Hettling; Jaap Heringa

doi:10.1093/bioinformatics/btq155

CGHnormaliter: a Bioconductor package for normalization of array CGH data with many CNAs

Bioinformatics. 2010 May 15;26(10):1366-7. doi: 10.1093/bioinformatics/btq155. Epub 2010 Apr 23.

Authors

Bart P P van Houte¹, Thomas W Binsl, Hannes Hettling, Jaap Heringa

Affiliation

¹ Centre for Integrative Bioinformatics VU, VU University Amsterdam, De Boelelaan 1081A, 1081 HV Amsterdam, The Netherlands.

PMID: 20418341
DOI: 10.1093/bioinformatics/btq155

Abstract

Summary: CGHnormaliter is a package for normalization of array comparative genomic hybridization (aCGH) data. It uses an iterative procedure that effectively eliminates the influence of imbalanced copy numbers. This leads to a more reliable assessment of copy number alterations (CNAs). CGHnormaliter is integrated in the Bioconductor environment allowing a smooth link to visualization tools and further data analysis.

Availability and implementation: The CGHnormaliter package is implemented in R and under GPL 3.0 license available at Bioconductor: http://www.bioconductor.org

Contact: heringa@few.vu.nl

Publication types

Research Support, Non-U.S. Gov't

MeSH terms

Comparative Genomic Hybridization / methods*
Databases, Genetic
Gene Expression Profiling
Oligonucleotide Array Sequence Analysis / methods*
Software*