High-Resolution Expression Map of the Arabidopsis Root Reveals Alternative Splicing and lincRNA Regulation

STAR: ultrafast universal RNA-seq aligner

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<tt>edgeR</tt> : a Bioconductor package for differential expression analysis of digital gene expression data

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featureCounts: an efficient general purpose program for assigning sequence reads to genomic features

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StringTie enables improved reconstruction of a transcriptome from RNA-seq reads

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TopHat2: accurate alignment of transcriptomes in the presence of insertions, deletions and gene fusions

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Life Sciences, Bioinformatics, Genetics +14