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the link to the PDF on http://bioconductor.org/packages/release/bioc/html/DESeq.html
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the link to the PDF on http://bioconductor.org/packages/release/bioc/html/DESeq.html
points to a file that does not exist: http://bioconductor.org/packages/release/bioc/manuals/DESeq/man/DESeq.pdf
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Indeed, it has been deprecated.