articleTop 1% cited
Transcript-level expression analysis of RNA-seq experiments with HISAT, StringTie and Ballgown
Nature Protocols · 2016 · Vol. 11(9) · pp. 1650–1667
Mihaela Pertea✉(Johns Hopkins University)Daehwan Kim(Johns Hopkins University)Geo Pertea(Johns Hopkins University)Jeffrey T. Leek(Johns Hopkins University)Steven L. Salzberg(Johns Hopkins University)
Genomics and Phylogenetic StudiesRNA modifications and cancerRNA and protein synthesis mechanismsRNA-SeqComputational biologyBiologySoftwareGeneComputer scienceTranscriptomeGene AnnotationRNAGenomics
MeSH terms
RNA, MessengerSoftwareStatistics as TopicUser-Computer InterfaceSequence Analysis, RNAGene Expression ProfilingMolecular Sequence Annotation
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References
Orchestrating high-throughput genomic analysis with Bioconductor
Nature Methods · 2015 · 3,927 citations
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BMC Bioinformatics · 2011 · 22,985 citations
Differential abundance analysis for microbial marker-gene surveys
Nature Methods · 2013 · 2,585 citations
Differential gene and transcript expression analysis of RNA-seq experiments with TopHat and Cufflinks
Nature Protocols · 2012 · 12,813 citations
HISAT: a fast spliced aligner with low memory requirements
Nature Methods · 2015 · 25,449 citations
Fast and accurate short read alignment with Burrows–Wheeler transform
Bioinformatics · 2009 · 61,752 citations
StringTie enables improved reconstruction of a transcriptome from RNA-seq reads
Nature Biotechnology · 2015 · 14,980 citations
<tt>edgeR</tt> : a Bioconductor package for differential expression analysis of digital gene expression data
Bioinformatics · 2009 · 43,721 citations
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