{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,10,17]],"date-time":"2025-10-17T19:49:46Z","timestamp":1760730586472},"reference-count":19,"publisher":"Oxford University Press (OUP)","issue":"12","content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2014,6,15]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Motivation: Studies of genomic DNA copy number alteration can deal with datasets with several million probes and thousands of subjects. Analyzing these data with currently available software (e.g. as available from BioConductor) can be extremely slow and may not be feasible because of memory requirements.<\/jats:p>\n               <jats:p>Results: We have developed a BioConductor package, ADaCGH2, that parallelizes the main segmentation algorithms (using forking on multicore computers or parallelization via message passing interface, etc., in clusters of computers) and uses ff objects for reading and data storage. We show examples of data with 6 million probes per array; we can analyze data that would otherwise not fit in memory, and compared with the non-parallelized versions we can achieve speedups of 25\u201340 times on a 64-cores machine.<\/jats:p>\n               <jats:p>Availability and implementation: ADaCGH2 is an R package available from BioConductor. Version 2.3.11 or higher is available from the development branch: http:\/\/www.bioconductor.org\/packages\/devel\/bioc\/html\/ADaCGH2.html.<\/jats:p>\n               <jats:p>Contact: \u00a0ramon.diaz@iib.uam.es<\/jats:p>\n               <jats:p>Supplementary information: \u00a0Supplementary data are available at Bioinformatics online.<\/jats:p>","DOI":"10.1093\/bioinformatics\/btu099","type":"journal-article","created":{"date-parts":[[2014,2,15]],"date-time":"2014-02-15T02:04:22Z","timestamp":1392429862000},"page":"1759-1761","source":"Crossref","is-referenced-by-count":1,"title":["ADaCGH2: parallelized analysis of (big) CNA data"],"prefix":"10.1093","volume":"30","author":[{"given":"Ramon","family":"Diaz-Uriarte","sequence":"first","affiliation":[{"name":"Department of Biochemistry, Universidad Aut\u00f3noma de Madrid, Instituto de Investigaciones Biom\u00e9dicas \u2018Alberto Sols\u2019 (UAM-CSIC), 28029 Madrid, Spain"}]}],"member":"286","published-online":{"date-parts":[[2014,2,14]]},"reference":[{"key":"2023012711061543100_btu099-B1","volume-title":"ff: Memory-Efficient Storage of Large Data on Disk and Fast Access Functions","author":"Adler","year":"2013"},{"key":"2023012711061543100_btu099-B2","doi-asserted-by":"crossref","first-page":"i139","DOI":"10.1093\/bioinformatics\/btn272","article-title":"A fast and flexible method for the segmentation of aCGH data","volume":"24","author":"Ben-Yaacov","year":"2008","journal-title":"Bioinformatics"},{"key":"2023012711061543100_btu099-B3","doi-asserted-by":"crossref","first-page":"W182","DOI":"10.1093\/nar\/gkq441","article-title":"waviCGH: a web application for the analysis and visualization of genomic copy number alterations","volume":"38","author":"Carro","year":"2010","journal-title":"Nucleic Acids Res."},{"key":"2023012711061543100_btu099-B4","doi-asserted-by":"crossref","first-page":"e737","DOI":"10.1371\/journal.pone.0000737","article-title":"ADaCGH: a parallelized web-based application and R package for the analysis of aCGH data","volume":"2","author":"Diaz-Uriarte","year":"2007","journal-title":"PLoS One"},{"key":"2023012711061543100_btu099-B5","doi-asserted-by":"crossref","first-page":"e59128","DOI":"10.1371\/journal.pone.0059128","article-title":"Comparative studies of copy number variation detection methods for next-generation sequencing technologies","volume":"8","author":"Duan","year":"2013","journal-title":"PLoS One"},{"key":"2023012711061543100_btu099-B6","doi-asserted-by":"crossref","first-page":"132","DOI":"10.1016\/j.jmva.2004.02.008","article-title":"Hidden Markov models approach to the analysis of array CGH data","volume":"90","author":"Fridlyand","year":"2004","journal-title":"J. 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