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waviCGH: a web application for the analysis and visualization of genomic copy number alterations

Angel Carro, Daniel Rico, Oscar M. Rueda, Ram�n D�az-Uriarte, David G. Pisano
2010 Nucleic Acids Research  
waviCGH is a versatile web server for the analysis and comparison of genomic copy number alterations in multiple samples from any species. waviCGH processes data generated by high density SNP-arrays, array-CGH  ...  or copy-number calls generated by any technique. waviCGH includes methods for pre-processing of the data, segmentation, calling of gains and losses, and minimal common regions determination over a set  ...  Eduardo Andres for his help deploying the web server. We are grateful to Kay Wang for all his help with the genomic waves adjustment method.  ... 
doi:10.1093/nar/gkq441 pmid:20507915 pmcid:PMC2896163 fatcat:jsj7tpobtzb3rbjc3oyqu6agla

FISH Oracle: a web server for flexible visualization of DNA copy number data in a genomic context

Malte Mader, Ronald Simon, Sascha Steinbiss, Stefan Kurtz
2011 Journal of Clinical Bioinformatics  
FISH Oracle will be instrumental to identify candidate onco and tumor suppressor genes based on the frequency and genomic position of DNA copy number changes.  ...  These features make the software especially suitable for the needs of life scientists. Conclusions: FISH Oracle offers a fast and easy to use visualization tool for array CGH and SNP array data.  ...  Acknowledgements This work was supported by a grant from the Werner-Otto-Stiftung to SK and RS (# 6/73) and a grant from the Federal Ministry of Education and Research (BMBF), Germany to RS (# FKZ 01GS08189  ... 
doi:10.1186/2043-9113-1-20 pmid:21884636 pmcid:PMC3164613 fatcat:vjmj5wf6gba2vap3vpmce567t4

Visualizing multidimensional cancer genomics data

Michael P Schroeder, Abel Gonzalez-Perez, Nuria Lopez-Bigas
2013 Genome Medicine  
Acknowledgements We acknowledge funding from the Spanish Ministry of Science and Technology (grant number SAF009-06954 and FPI fellowship assigned to MPS), and from the Spanish National Institute of Bioinformatics  ...  We are thankful to Elaine M Lilly for assistance with language editing.  ...  web technologies, whereas Genome Alteration Print [29] is a desktop application.  ... 
doi:10.1186/gm413 pmid:23363777 pmcid:PMC3706894 fatcat:o5pz2lusezcsdilwoauf65e3vi

Analysis of Molecular Cytogenetic Alteration in Rhabdomyosarcoma by Array Comparative Genomic Hybridization

Chunxia Liu, Dongliang Li, Jinfang Jiang, Jianming Hu, Wei Zhang, Yunzhao Chen, Xiaobin Cui, Yan Qi, Hong Zou, WenJie Zhang, Feng Li, Roberto Amendola
2014 PLoS ONE  
In conclusion, this study identified a number of CNVs in RMS and functional analyses showed enrichment for genes and miRNAs located in these CNVs regions.  ...  We then performed bioinformatics-based functional enrichment analysis for genes located in the genomic regions with CNVs.  ...  interrogation of hundreds of genomic loci for DNA copy number gains and losses.  ... 
doi:10.1371/journal.pone.0094924 pmid:24743780 pmcid:PMC3990535 fatcat:t3v7qh5gdreqlbjp6uhrfuwu4i