exomeCopy R package is for detection of copy number variants (CNV) from exome and unpaired sample sequencing. The implementation is based on a hidden Markov model on background read depth and GC-content to normalize copy count.
Exome sequencing
Love MI, Myšičková A, Sun R, Kalscheuer V, Vingron M, Haas SA "Modeling read counts for CNV detection in exome sequencing data." Stat Appl Genet Mol Biol. 2011 Nov 8;10(1). pii: /j/sagmb.2011.10.issue-1/1544-6115.1732/1544-6115.1732.xml. https://doi.org/10.2202/1544-6115.1732
PMID: 23089826
PMCID: PMC3517018
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
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