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Volumn 9, Issue 1, 2014, Pages

Segmentor3IsBack: An R package for the fast and exact segmentation of Seq-data

Author keywords

Count data; Data compression; Exact algorithm; Fast algorithm; Genome annotation; RNA Seq data; Segmentation algorithm

Indexed keywords


EID: 84897935670     PISSN: None     EISSN: 17487188     Source Type: Journal    
DOI: 10.1186/1748-7188-9-6     Document Type: Article
Times cited : (23)

References (28)
  • 1
    • 0347503105 scopus 로고    scopus 로고
    • Statistical methods for DNA sequence segmentation
    • Braun JV, Muller HG. Statistical methods for DNA sequence segmentation. Stat Sci 1998, 13(2):142-162.
    • (1998) Stat Sci , vol.13 , Issue.2 , pp. 142-162
    • Braun, J.V.1    Muller, H.G.2
  • 2
    • 78149448100 scopus 로고    scopus 로고
    • Estimating the joint distribution of independent categorical variables via model selection
    • Durot C, Lebarbier E, Tocquet AS. Estimating the joint distribution of independent categorical variables via model selection. Bernoulli 2009, 15:475-507.
    • (2009) Bernoulli , vol.15 , pp. 475-507
    • Durot, C.1    Lebarbier, E.2    Tocquet, A.S.3
  • 4
    • 84864951336 scopus 로고    scopus 로고
    • Reconstructing DNA copy number by joint segmentation of multiple sequences
    • 10.1186/1471-2105-13-205, 3534631, 22897923
    • Zhang Z, Lange K, Sabatti C. Reconstructing DNA copy number by joint segmentation of multiple sequences. BMC Bioinformatics 2012, 13:205. 10.1186/1471-2105-13-205, 3534631, 22897923.
    • (2012) BMC Bioinformatics , vol.13 , pp. 205
    • Zhang, Z.1    Lange, K.2    Sabatti, C.3
  • 5
    • 52949087226 scopus 로고    scopus 로고
    • A fast Bayesian change point analysis for the segmentation of microarray data
    • 10.1093/bioinformatics/btn404, 18667443
    • Erdman C, Emerson JW. A fast Bayesian change point analysis for the segmentation of microarray data. Bioinformatics 2008, 24(19):2143-2148. 10.1093/bioinformatics/btn404, 18667443.
    • (2008) Bioinformatics , vol.24 , Issue.19 , pp. 2143-2148
    • Erdman, C.1    Emerson, J.W.2
  • 6
    • 3543105225 scopus 로고    scopus 로고
    • Circular binary segmentation for the analysis of array-based DNA copy number data
    • Olshen AB, Venkatraman ES, Lucito R, Wigler M. Circular binary segmentation for the analysis of array-based DNA copy number data. Biostat (Oxford, England) 2004, 5(4):557-572.
    • (2004) Biostat (Oxford, England) , vol.5 , Issue.4 , pp. 557-572
    • Olshen, A.B.1    Venkatraman, E.S.2    Lucito, R.3    Wigler, M.4
  • 7
    • 25444531432 scopus 로고    scopus 로고
    • A statistical approach for array CGH data analysis
    • 10.1186/1471-2105-6-27, 549559, 15705208
    • Picard F, Robin S, Lavielle M, Vaisse C, Daudin J. A statistical approach for array CGH data analysis. BMC Bioinformatics 2005, 6:27. 10.1186/1471-2105-6-27, 549559, 15705208.
    • (2005) BMC Bioinformatics , vol.6 , pp. 27
    • Picard, F.1    Robin, S.2    Lavielle, M.3    Vaisse, C.4    Daudin, J.5
  • 8
    • 79959397907 scopus 로고    scopus 로고
    • Joint segmentation, calling and normalization of multiple CGH profiles
    • 10.1093/biostatistics/kxq076, 21209153
    • Picard F, Lebarbier E, Hoebeke M, Rigaill G, Thiam B, Robin S. Joint segmentation, calling and normalization of multiple CGH profiles. Biostatistics 2011, 12(3):413-428. 10.1093/biostatistics/kxq076, 21209153.
    • (2011) Biostatistics , vol.12 , Issue.3 , pp. 413-428
    • Picard, F.1    Lebarbier, E.2    Hoebeke, M.3    Rigaill, G.4    Thiam, B.5    Robin, S.6
  • 10
    • 64849083125 scopus 로고    scopus 로고
    • CNV-seq, a new method to detect copy number variation using high-throughput sequencing
    • 10.1186/1471-2105-10-80, 2667514, 19267900
    • Xie C, Tammi MT. CNV-seq, a new method to detect copy number variation using high-throughput sequencing. BMC Bioinformatics 2009, 10:80. 10.1186/1471-2105-10-80, 2667514, 19267900.
    • (2009) BMC Bioinformatics , vol.10 , pp. 80
    • Xie, C.1    Tammi, M.T.2
  • 11
    • 69749122557 scopus 로고    scopus 로고
    • Sensitive and accurate detection of copy number variants using read depth of coverage
    • 10.1101/gr.092981.109, 2752127, 19657104
    • Yoon S, Xuan Z, Makarov V, Ye K, Sebat J. Sensitive and accurate detection of copy number variants using read depth of coverage. Genome Res 2009, 19:1586-1592. 10.1101/gr.092981.109, 2752127, 19657104.
    • (2009) Genome Res , vol.19 , pp. 1586-1592
    • Yoon, S.1    Xuan, Z.2    Makarov, V.3    Ye, K.4    Sebat, J.5
  • 13
    • 84866240316 scopus 로고    scopus 로고
    • Change-point model on nonhomogeneous Poisson processes with application in copy number profiling by next-generation DNA sequencing
    • Shen JJ, Zhang NR. Change-point model on nonhomogeneous Poisson processes with application in copy number profiling by next-generation DNA sequencing. Ann Appl Stat 2012, 6(2):476-496.
    • (2012) Ann Appl Stat , vol.6 , Issue.2 , pp. 476-496
    • Shen, J.J.1    Zhang, N.R.2
  • 14
    • 84888133730 scopus 로고    scopus 로고
    • Optimal detection of a jump in the intensity of a Poisson process or in a density with likelihood ratio statistics
    • Rivera C, Walther G. Optimal detection of a jump in the intensity of a Poisson process or in a density with likelihood ratio statistics. Scand J Stat 2013, 40(4):752-769.
    • (2013) Scand J Stat , vol.40 , Issue.4 , pp. 752-769
    • Rivera, C.1    Walther, G.2
  • 15
  • 16
    • 84871961490 scopus 로고    scopus 로고
    • Optimal detection of changepoints with a linear computational cost
    • Killick R, Fearnhead P, Eckley I. Optimal detection of changepoints with a linear computational cost. J Am Stat Assoc 2012, 107(500):1590-1598.
    • (2012) J Am Stat Assoc , vol.107 , Issue.500 , pp. 1590-1598
    • Killick, R.1    Fearnhead, P.2    Eckley, I.3
  • 18
    • 84983160862 scopus 로고    scopus 로고
    • Pruned dynamic programming for optimal multiple change-point detection
    • Rigaill G. Pruned dynamic programming for optimal multiple change-point detection. Arxiv:1004.0887 2010, [http://arxiv.org/abs/1004.0887].
    • (2010) Arxiv:1004.0887
    • Rigaill, G.1
  • 20
    • 83455238345 scopus 로고    scopus 로고
    • GC-Content normalization for RNA-Seq data
    • 10.1186/1471-2105-12-480, 3315510, 22177264
    • Risso D, Schwartz K, Sherlock G, Dudoit S. GC-Content normalization for RNA-Seq data. BMC Bioinformatics 2011, 12:480. 10.1186/1471-2105-12-480, 3315510, 22177264.
    • (2011) BMC Bioinformatics , vol.12 , pp. 480
    • Risso, D.1    Schwartz, K.2    Sherlock, G.3    Dudoit, S.4
  • 21
    • 77949481052 scopus 로고    scopus 로고
    • Evaluation of statistical methods for normalization and differential expression in mRNA-Seq experiments
    • 10.1186/1471-2105-11-94, 2838869, 20167110
    • Bullard J, Purdom E, Hansen K, Dudoit S. Evaluation of statistical methods for normalization and differential expression in mRNA-Seq experiments. BMC Bioinformatics 2010, 11:94. 10.1186/1471-2105-11-94, 2838869, 20167110.
    • (2010) BMC Bioinformatics , vol.11 , pp. 94
    • Bullard, J.1    Purdom, E.2    Hansen, K.3    Dudoit, S.4
  • 22
    • 0016355478 scopus 로고
    • A new look at the statistical model identification
    • Akaike H. A new look at the statistical model identification. Automatic Control IEEE Trans 1974, 19(6):716-723.
    • (1974) Automatic Control IEEE Trans , vol.19 , Issue.6 , pp. 716-723
    • Akaike, H.1
  • 23
    • 0009728860 scopus 로고
    • Estimation of a noisy discrete-time step function: Bayes and empirical Bayes approaches
    • Yao Y. Estimation of a noisy discrete-time step function: Bayes and empirical Bayes approaches. Ann Stat 1984, 12(4):1434-1447.
    • (1984) Ann Stat , vol.12 , Issue.4 , pp. 1434-1447
    • Yao, Y.1
  • 24
    • 34247243220 scopus 로고    scopus 로고
    • A modified Bayes information criterion with applications to the analysis of comparative genomic hybridization data
    • [PMID: 17447926], 10.1111/j.1541-0420.2006.00662.x, 17447926
    • Zhang NR, Siegmund DO. A modified Bayes information criterion with applications to the analysis of comparative genomic hybridization data. Biometrics 2007, 63:22-32. [PMID: 17447926], 10.1111/j.1541-0420.2006.00662.x, 17447926.
    • (2007) Biometrics , vol.63 , pp. 22-32
    • Zhang, N.R.1    Siegmund, D.O.2
  • 25
    • 85006306469 scopus 로고    scopus 로고
    • Segmentation of the poisson and negative binomial rate models: a penalized estimator
    • arXiv preprint arXiv:1301.2534
    • Cleynen A, Lebarbier E. Segmentation of the poisson and negative binomial rate models: a penalized estimator. Esaim: P & S 2014, arXiv preprint arXiv:1301.2534.
    • (2014) Esaim: P & S
    • Cleynen, A.1    Lebarbier, E.2
  • 26
    • 13844315857 scopus 로고    scopus 로고
    • Detecting multiple change-points in the mean of Gaussian process by model selection
    • Lebarbier E. Detecting multiple change-points in the mean of Gaussian process by model selection. Signal Process 2005, 85(4):717-736.
    • (2005) Signal Process , vol.85 , Issue.4 , pp. 717-736
    • Lebarbier, E.1
  • 27
    • 61749091779 scopus 로고    scopus 로고
    • Data-driven calibration of penalties for least-squares regression
    • (electronic)
    • Arlot S, Massart P. Data-driven calibration of penalties for least-squares regression. J Mach Learn Res 2009, 10:245-279. (electronic).
    • (2009) J Mach Learn Res , vol.10 , pp. 245-279
    • Arlot, S.1    Massart, P.2
  • 28
    • 84880382996 scopus 로고    scopus 로고
    • Fast estimation of posterior probabilities in change-point analysis through a constrained hidden Markov model
    • Luong TM, Rozenholc Y, Nuel G. Fast estimation of posterior probabilities in change-point analysis through a constrained hidden Markov model. Comput Stat Data Anal 2013,
    • (2013) Comput Stat Data Anal
    • Luong, T.M.1    Rozenholc, Y.2    Nuel, G.3


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.