Count-based differential expression analysis of RNA sequencing data using R and Bioconductor
出版年份 2013 全文链接
标题
Count-based differential expression analysis of RNA sequencing data using R and Bioconductor
作者
关键词
-
出版物
Nature Protocols
Volume 8, Issue 9, Pages 1765-1786
出版商
Springer Nature America, Inc
发表日期
2013-08-23
DOI
10.1038/nprot.2013.099
参考文献
相关参考文献
注意:仅列出部分参考文献,下载原文获取全部文献信息。- A comparison of methods for differential expression analysis of RNA-seq data
- (2013) Charlotte Soneson et al. BMC BIOINFORMATICS
- The Arabidopsis Nucleosome Remodeler DDM1 Allows DNA Methyltransferases to Access H1-Containing Heterochromatin
- (2013) Assaf Zemach et al. CELL
- Rev-Erbs repress macrophage gene expression by inhibiting enhancer-directed transcription
- (2013) Michael T. Y. Lam et al. NATURE
- The Subread aligner: fast, accurate and scalable read mapping by seed-and-vote
- (2013) Yang Liao et al. NUCLEIC ACIDS RESEARCH
- easyRNASeq: a bioconductor package for processing RNA-Seq data
- (2012) N. Delhomme et al. BIOINFORMATICS
- Identifying differentially expressed transcripts from RNA-seq data with biological variation
- (2012) Peter Glaus et al. BIOINFORMATICS
- Tools for mapping high-throughput sequencing data
- (2012) Nuno A. Fonseca et al. BIOINFORMATICS
- STAR: ultrafast universal RNA-seq aligner
- (2012) Alexander Dobin et al. BIOINFORMATICS
- Bayesian analysis of RNA sequencing data by estimating multiple shrinkage priors
- (2012) M. A. Van De Wiel et al. BIOSTATISTICS
- Removing technical variability in RNA-seq data using conditional quantile normalization
- (2012) K. D. Hansen et al. BIOSTATISTICS
- A new shrinkage estimator for dispersion improves differential expression detection in RNA-seq data
- (2012) H. Wu et al. BIOSTATISTICS
- Integrative Genomics Viewer (IGV): high-performance genomics data visualization and exploration
- (2012) H. Thorvaldsdottir et al. BRIEFINGS IN BIOINFORMATICS
- Foxp3 Exploits a Pre-Existent Enhancer Landscape for Regulatory T Cell Lineage Specification
- (2012) Robert M. Samstein et al. CELL
- Copy-number-aware differential analysis of quantitative DNA sequencing data
- (2012) M. D. Robinson et al. GENOME RESEARCH
- Detecting differential usage of exons from RNA-seq data
- (2012) S. Anders et al. GENOME RESEARCH
- Differential oestrogen receptor binding is associated with clinical outcome in breast cancer
- (2012) Caryn S. Ross-Innes et al. NATURE
- Epigenetic expansion of VHL-HIF signal output drives multiorgan metastasis in renal cancer
- (2012) Sakari Vanharanta et al. NATURE MEDICINE
- Differential gene and transcript expression analysis of RNA-seq experiments with TopHat and Cufflinks
- (2012) Cole Trapnell et al. Nature Protocols
- A comprehensive comparison of RNA-Seq-based transcriptome analysis from reads to differential gene expression and cross-comparison with microarrays: a case study in Saccharomyces cerevisiae
- (2012) Intawat Nookaew et al. NUCLEIC ACIDS RESEARCH
- Differential expression analysis of multifactor RNA-Seq experiments with respect to biological variation
- (2012) Davis J. McCarthy et al. NUCLEIC ACIDS RESEARCH
- Proteomic Analysis Reveals New Cardiac-Specific Dystrophin-Associated Proteins
- (2012) Eric K. Johnson et al. PLoS One
- Detecting Differential Expression in RNA-sequence Data Using Quasi-likelihood with Shrunken Dispersion Estimates
- (2012) Steven P. Lund et al. Statistical Applications in Genetics and Molecular Biology
- A powerful and flexible approach to the analysis of RNA sequence count data
- (2011) Yi-Hui Zhou et al. BIOINFORMATICS
- Using control genes to correct for unwanted variation in microarray data
- (2011) J. A. Gagnon-Bartsch et al. BIOSTATISTICS
- GC-Content Normalization for RNA-Seq Data
- (2011) Davide Risso et al. BMC BIOINFORMATICS
- Differential expression in RNA-seq: A matter of depth
- (2011) S. Tarazona et al. GENOME RESEARCH
- Sequencing technology does not eliminate biological variability
- (2011) Kasper D Hansen et al. NATURE BIOTECHNOLOGY
- Full-length transcriptome assembly from RNA-Seq data without a reference genome
- (2011) Manfred G Grabherr et al. NATURE BIOTECHNOLOGY
- Preferred analysis methods for single genomic regions in RNA sequencing revealed by processing the shape of coverage
- (2011) Michał J. Okoniewski et al. NUCLEIC ACIDS RESEARCH
- Human immunodeficiency virus-1 Tat activates NF-κB via physical interaction with IκB-α and p65
- (2011) Giuseppe Fiume et al. NUCLEIC ACIDS RESEARCH
- Differential Gene Expression in the Siphonophore Nanomia bijuga (Cnidaria) Assessed with Multiple Next-Generation Sequencing Workflows
- (2011) Stefan Siebert et al. PLoS One
- Savant: genome browser for high-throughput sequencing data
- (2010) M. Fiume et al. BIOINFORMATICS
- Fast and SNP-tolerant detection of complex variants and splicing in short reads
- (2010) T. D. Wu et al. BIOINFORMATICS
- Evaluation of statistical methods for normalization and differential expression in mRNA-Seq experiments
- (2010) James H Bullard et al. BMC BIOINFORMATICS
- baySeq: Empirical Bayesian methods for identifying differential expression in sequence count data
- (2010) Thomas J Hardcastle et al. BMC BIOINFORMATICS
- Statistical Design and Analysis of RNA Sequencing Data
- (2010) P. L. Auer et al. GENETICS
- Conservation of an RNA regulatory map between Drosophila and mammals
- (2010) A. N. Brooks et al. GENOME RESEARCH
- Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation
- (2010) Cole Trapnell et al. NATURE BIOTECHNOLOGY
- Tackling the widespread and critical impact of batch effects in high-throughput data
- (2010) Jeffrey T. Leek et al. NATURE REVIEWS GENETICS
- MapSplice: Accurate mapping of RNA-seq reads for splice junction discovery
- (2010) Kai Wang et al. NUCLEIC ACIDS RESEARCH
- Independent filtering increases detection power for high-throughput experiments
- (2010) R. Bourgon et al. PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
- A scaling normalization method for differential expression analysis of RNA-seq data
- (2010) Mark D Robinson et al. GENOME BIOLOGY
- Differential expression analysis for sequence count data
- (2010) Simon Anders et al. GENOME BIOLOGY
- ShortRead: a bioconductor package for input, quality assessment and exploration of high-throughput sequence data
- (2009) M. Morgan et al. BIOINFORMATICS
- TopHat: discovering splice junctions with RNA-Seq
- (2009) Cole Trapnell et al. BIOINFORMATICS
- The Sequence Alignment/Map format and SAMtools
- (2009) H. Li et al. BIOINFORMATICS
- edgeR: a Bioconductor package for differential expression analysis of digital gene expression data
- (2009) M. D. Robinson et al. BIOINFORMATICS
- Sex-specific and lineage-specific alternative splicing in primates
- (2009) R. Blekhman et al. GENOME RESEARCH
- How to map billions of short reads onto genomes
- (2009) Cole Trapnell et al. NATURE BIOTECHNOLOGY
- Mapping and quantifying mammalian transcriptomes by RNA-Seq
- (2008) Ali Mortazavi et al. NATURE METHODS
- RNA-Seq: a revolutionary tool for transcriptomics
- (2008) Zhong Wang et al. NATURE REVIEWS GENETICS
Find the ideal target journal for your manuscript
Explore over 38,000 international journals covering a vast array of academic fields.
SearchBecome a Peeref-certified reviewer
The Peeref Institute provides free reviewer training that teaches the core competencies of the academic peer review process.
Get Started