TITAN is a tool for estimation of copy number variation (CNV) and loss of heterozygosity (LOH) in whole-genome sequencing data consisting of clonal cell populations. The TITAN algorithm uses hidden Marlov model (HMM).
Alternative name: TitanCNA
Genetics; Whole genome sequencing; DNA structural variation; Oncology
Ha G, Roth A, Khattra J, Ho J, Yap D, Prentice LM, Melnyk N, McPherson A, Bashashati A, Laks E, Biele J, Ding J, Le A, Rosner J, Shumansky K, Marra MA, Gilks CB, Huntsman DG, McAlpine JN, Aparicio S, Shah SP "TITAN: inference of copy number architectures in clonal cell populations from tumor whole-genome sequence data." Genome Res. 2014 Nov;24(11):1881-93. 24. https://doi.org/10.1101/gr.180281.114
PMID: 25060187
PMCID: PMC4216928
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