cn.farms is an R package for copy number variation (CNV) analysis of the Affymetrix (250K-SNP6.0) array types. It uses snow and ff.
Genetic variation
Clevert DA, Mitterecker A, Mayr A, Klambauer G, Tuefferd M, De Bondt A, Talloen W, Göhlmann H, Hochreiter S "cn.FARMS: a latent variable model to detect copy number variations in microarray data with a low false discovery rate" Nucleic Acids Res. 2011 Jul;39(12):e79. https://doi.org/10.1093/nar/gkr197
PMID: 21486749
PMCID: PMC3130288
Huber W, Carey VJ, Gentleman R, Anders S, Carlson M, Carvalho BS, Bravo HC, Davis S, Gatto L, Girke T, Gottardo R, Hahne F, Hansen KD, Irizarry RA, Lawrence M, Love MI, MacDonald J1, Obenchain V, Oleś AK, Pagès H, Reyes A, Shannon P, Smyth GK, Tenenbaum D, Waldron L, Morgan M "Orchestrating high-throughput genomic analysis with Bioconductor." Nat Methods. 2015 Feb;12(2):115-21. https://doi.org/10.1038/nmeth.3252
PMID: 25633503
PMCID: PMC4509590
Gentleman RC, Carey VJ, Bates DM, Bolstad B, Dettling M, Dudoit S, Ellis B, Gautier L, Ge Y, Gentry J, Hornik K, Hothorn T, Huber W, Iacus S, Irizarry R, Leisch F, Li C, Maechler M, Rossini AJ, Sawitzki G, Smith C, Smyth G, Tierney L, Yang JY, Zhang J. "Bioconductor: open software development for computational biology and bioinformatics." Genome Biol. 2004;5(10):R80. Epub 2004 Sep 15. https://doi.org/10.1186/gb-2004-5-10-r80
PMID: 15461798
PMCID: PMC545600
If you find errors, please report here.
SECTIONS
TutorialsFind thousands of Bioinformatics and Life Science software tools and databases in the newly launched
Ads