... expression¹

Such as DESeq[2], DESeq2[3] or edgeR[4]

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... tools²

Such as DEXSeq[5] or http://hartleys.github.io/JunctionSeq/JunctionSeq

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... gtf³

Which can be acquired from the Ensembl website at http://www.ensembl.org

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... specification⁴

See the gtf file specification at http://genome.ucsc.edu/FAQ/FAQformat.html

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... documentation⁵

Found http://hartleys.github.io/QoRTs/jarHtml/QC.htmlhere.

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... utility⁶

Found here: http://hartleys.github.io/QoRTs/jarHtml/index.html

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... documentation⁷

Found here: http://hartleys.github.io/QoRTs/jarHtml/index.html

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... documentation⁸

Found here: http://hartleys.github.io/QoRTs/jarHtml/index.html

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... documentation⁹

Found here: http://hartleys.github.io/QoRTs/jarHtml/mergeWig.html

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... documentation¹⁰

Found here: http://hartleys.github.io/QoRTs/jarHtml/makeJunctionTrack.html

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... documentation¹¹

Found here: http://hartleys.github.io/QoRTs/jarHtml/makeJunctionTrack.html

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... documentation¹²

Found here: http://hartleys.github.io/QoRTs/jarHtml/makeJunctionTrack.html

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