article Open AccessTop 1% cited
Differential gene and transcript expression analysis of RNA-seq experiments with TopHat and Cufflinks
Nature Protocols · 2012 · Vol. 7(3) · pp. 562–578
Cole Trapnell✉(Broad Institute)Adam Roberts(University of California, Berkeley)Loyal A. Goff(Broad Institute)Geo Pertea(Johns Hopkins University)Daehwan Kim(Johns Hopkins University)David R. Kelley(Harvard University)Harold Pimentel(University of California, Berkeley)Steven L. Salzberg(Johns Hopkins Medicine)John L. Rinn(Harvard University)Lior Pachter(University of California, Berkeley)
Genomics and Phylogenetic StudiesRNA modifications and cancerRNA Research and SplicingRNA-SeqComputational biologyBiologyComputer scienceGeneTranscriptomespliceReference genomeRNA splicingSoftware
MeSH terms
SoftwareSequence Analysis, DNADNA, ComplementaryGene Expression ProfilingGenomicsGenetic Association Studies
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References
Integrative genomics viewer
Nature Biotechnology · 2011 · 16,203 citations
TopHat: discovering splice junctions with RNA-Seq
Bioinformatics · 2009 · 12,093 citations
The Sequence Alignment/Map format and SAMtools
Bioinformatics · 2009 · 66,208 citations
<tt>edgeR</tt> : a Bioconductor package for differential expression analysis of digital gene expression data
Bioinformatics · 2009 · 43,721 citations
DEGseq: an R package for identifying differentially expressed genes from RNA-seq data
Bioinformatics · 2009 · 4,836 citations
RNA-seq: An assessment of technical reproducibility and comparison with gene expression arrays
Genome Research · 2008 · 2,821 citations
Ultrafast and memory-efficient alignment of short DNA sequences to the human genome
Genome biology · 2009 · 22,766 citations
Full-length transcriptome assembly from RNA-Seq data without a reference genome
Nature Biotechnology · 2011 · 22,340 citations
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