MultiRankSeq: Multiperspective Approach for RNAseq Differential Expression Analysis and Quality Control
作者： Yan Guo , Shilin Zhao , Fei Ye , Quanhu Sheng , Yu Shyr
DOI: 10.1155/2014/248090
关键词:
摘要: … We demonstrate MultiRankSeq using two example datasets from the TCGA breast cancer … normal tissues from same patients (TCGA-A7-A0D9, TCGA-BH-A0B3, and TCGA-BH-A0BJ). …
hindawi.com参考文章(32)
Yu Shyr, KyungMann Kim, Weighted Flexible Compound Covariate Method for Classifying Microarray Data Springer, Boston, MA. pp. 186- 200 ,(2003) , 10.1007/0-306-47815-3_10
Paul L. Auer, Rebecca W Doerge, A Two-Stage Poisson Model for Testing RNA-Seq Data Statistical Applications in Genetics and Molecular Biology. ,vol. 10, pp. 1- 26 ,(2011) , 10.2202/1544-6115.1627
Yanming Di, Daniel W Schafer, Jason S Cumbie, Jeff H Chang, The NBP Negative Binomial Model for Assessing Differential Gene Expression from RNA-Seq Statistical Applications in Genetics and Molecular Biology. ,vol. 10, pp. 1- 28 ,(2011) , 10.2202/1544-6115.1637
Yan Guo, Chung-I Li, Fei Ye, Yu Shyr, Evaluation of read count based RNAseq analysis methods BMC Genomics. ,vol. 14, pp. 1- 8 ,(2013) , 10.1186/1471-2164-14-S8-S2
Zhong Wang, Mark Gerstein, Michael Snyder, RNA-Seq: a revolutionary tool for transcriptomics Nature Reviews Genetics. ,vol. 10, pp. 57- 63 ,(2009) , 10.1038/NRG2484
Jay Shendure, The Beginning of the End for Microarrays Nature Methods. ,vol. 5, pp. 585- 587 ,(2008) , 10.1038/NMETH0708-585
W. J. Conover, Mark E. Johnson, Myrle M. Johnson, A Comparative Study of Tests for Homogeneity of Variances, with Applications to the Outer Continental Shelf Bidding Data Technometrics. ,vol. 23, pp. 351- 361 ,(1981) , 10.1080/00401706.1981.10487680
Thomas J Hardcastle, Krystyna A Kelly, baySeq: Empirical Bayesian methods for identifying differential expression in sequence count data BMC Bioinformatics. ,vol. 11, pp. 422- 422 ,(2010) , 10.1186/1471-2105-11-422
Bo Li, Colin N Dewey, RSEM: accurate transcript quantification from RNA-Seq data with or without a reference genome BMC Bioinformatics. ,vol. 12, pp. 323- 323 ,(2011) , 10.1186/1471-2105-12-323
Y. Guo, F. Ye, Q. Sheng, T. Clark, D. C. Samuels, Three-stage quality control strategies for DNA re-sequencing data Briefings in Bioinformatics. ,vol. 15, pp. 879- 889 ,(2014) , 10.1093/BIB/BBT069