Efficient experimental design and analysis strategies for the detection of differential expression using RNA-Sequencing

References

Page 1

	Year	Citations
<tt>edgeR</tt> : a Bioconductor package for differential expression analysis of digital gene expression data Mark D. Robinson, Davis J. McCarthy, Gordon K. Smyth Bioinformatics	2009	42.7K
RSEM: accurate transcript quantification from RNA-Seq data with or without a reference genome Bo Li, Colin N. Dewey BMC Bioinformatics	2011	22.5K
Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation Cole Trapnell, Brian A. Williams, Geo Pertea, Nature Biotechnology Developmental BiologyFunctional GenomicsRna BiologyRna-seq RevealsTranscriptomics Technology	2010	16.1K
Differential expression analysis for sequence count data Simon Anders, Wolfgang Huber Genome biology EngineeringGenomicsGene Expression ProfilingHigh Throughput SequencingDifferential Expression Analysis	2010	16.1K
Mapping and quantifying mammalian transcriptomes by RNA-Seq A Mortazavi, Brian A. Williams, Kenneth McCue, Nature Methods Functional GenomicsGeneticsTranscriptomics TechnologyMammalian TranscriptomesLong Non-coding Rna	2008	14K
A scaling normalization method for differential expression analysis of RNA-seq data Mark D. Robinson, Alicia Oshlack Genome biology	2010	8.2K
Deep surveying of alternative splicing complexity in the human transcriptome by high-throughput sequencing Qun Pan, Ofer Shai, Leo J. Lee, Nature Genetics Long-read SequencingFunctional GenomicsDeep SurveyingGeneticsHigh-throughput Sequencing	2008	3.9K
VennDiagram: a package for the generation of highly-customizable Venn and Euler diagrams in R Hanbo Chen, Paul C. Boutros BMC Bioinformatics	2011	3.1K
RNA-seq: An assessment of technical reproducibility and comparison with gene expression arrays John C. Marioni, Christopher E. Mason, Shrikant Mane, Genome Research GeneticsMolecular BiologyTranscriptomics TechnologyIllumina SequencingGenomics	2008	2.8K
Improving RNA-Seq expression estimates by correcting for fragment bias Adam Roberts, Cole Trapnell, Julie Donaghey, Genome biology	2011	1.8K

Page 1