A fuzzy method for RNA-Seq differential expression analysis in presence of multireads
暂无分享,去创建一个
Corrado Mencar | Giorgio Grillo | Sabino Liuni | Arianna Consiglio | Mariano Francesco Caratozzolo | Flaviana Marzano | S. Liuni | M. F. Caratozzolo | F. Marzano | G. Grillo | A. Consiglio | Corrado Mencar
[1] James G. R. Gilbert,et al. The vertebrate genome annotation (Vega) database , 2004, Nucleic Acids Res..
[2] Lior Pachter,et al. Near-optimal RNA-Seq quantification , 2015, ArXiv.
[3] Mick Watson,et al. Errors in RNA-Seq quantification affect genes of relevance to human disease , 2015, Genome Biology.
[4] B. Williams,et al. Mapping and quantifying mammalian transcriptomes by RNA-Seq , 2008, Nature Methods.
[5] Shankar Subramaniam,et al. Evaluation of normalization methods in mammalian microRNA-Seq data. , 2012, RNA.
[6] Hideaki Sugawara,et al. The Sequence Read Archive , 2010, Nucleic Acids Res..
[7] Didier Dubois,et al. Possibility Theory, Probability Theory and Multiple-Valued Logics: A Clarification , 2001, Annals of Mathematics and Artificial Intelligence.
[8] Ion I. Mandoiu,et al. Estimation of alternative splicing isoform frequencies from RNA-Seq data , 2010, Algorithms for Molecular Biology.
[9] L. Zadeh. Fuzzy sets as a basis for a theory of possibility , 1999 .
[10] W. Pedrycz,et al. An introduction to fuzzy sets : analysis and design , 1998 .
[11] Peng Cui,et al. Dynamic regulation of genome-wide pre-mRNA splicing and stress tolerance by the Sm-like protein LSm5 in Arabidopsis , 2014, Genome Biology.
[12] Yan Mei,et al. The RNA-binding protein hnRNPLL induces a T cell alternative splicing program delineated by differential intron retention in polyadenylated RNA , 2014, Genome Biology.
[13] Lior Pachter,et al. Near-optimal probabilistic RNA-seq quantification , 2016, Nature Biotechnology.
[14] T. Aune,et al. Defective structural RNA processing in relapsing-remitting multiple sclerosis , 2015, Genome Biology.
[15] M. Gerstein,et al. RNA-Seq: a revolutionary tool for transcriptomics , 2009, Nature Reviews Genetics.
[16] Ying Jin,et al. TEtranscripts: a package for including transposable elements in differential expression analysis of RNA-seq datasets , 2015, Bioinform..
[17] Thomas L. Madden,et al. The BLAST Sequence Analysis Tool , 2013 .
[18] Gonçalo R. Abecasis,et al. The Sequence Alignment/Map format and SAMtools , 2009, Bioinform..
[19] Colin N. Dewey,et al. RSEM: accurate transcript quantification from RNA-Seq data with or without a reference genome , 2011, BMC Bioinformatics.
[20] Nicolas Servant,et al. A comprehensive evaluation of normalization methods for Illumina high-throughput RNA sequencing data analysis , 2013, Briefings Bioinform..
[21] W. Huber,et al. Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2 , 2014, Genome Biology.
[22] Geet Duggal,et al. Salmon: Accurate, Versatile and Ultrafast Quantification from RNA-seq Data using Lightweight-Alignment , 2015 .
[23] Michaela Frye,et al. Beyond library size: a field guide to NGS normalization , 2014, bioRxiv.
[24] Y. Benjamini,et al. Controlling the false discovery rate: a practical and powerful approach to multiple testing , 1995 .
[25] David R. Kelley,et al. Differential gene and transcript expression analysis of RNA-seq experiments with TopHat and Cufflinks , 2012, Nature Protocols.
[26] Colin N. Dewey,et al. RNA-Seq gene expression estimation with read mapping uncertainty , 2009, Bioinform..
[27] Mark D. Robinson,et al. edgeR: a Bioconductor package for differential expression analysis of digital gene expression data , 2009, Bioinform..
[28] Marc W. Schmid,et al. Rcount: simple and flexible RNA-Seq read counting , 2015, Bioinform..
[29] R. Loewe. Combinational usage of next generation sequencing and qPCR for the analysis of tumor samples. , 2013, Methods.
[30] Geoffrey J Faulkner,et al. A rescue strategy for multimapping short sequence tags refines surveys of transcriptional activity by CAGE. , 2008, Genomics.
[31] Gunnar Rätsch,et al. MMR: a tool for read multi-mapper resolution , 2015, bioRxiv.
[32] Robert LIN,et al. NOTE ON FUZZY SETS , 2014 .