Bioconductor Seqlevels

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3.0k

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granges seqlevels feature request

updated 3.4 years ago by story.benjamin ▴ 20 • written 8.5 years ago by Charles Plessy ▴ 180

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2.0k

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txdb.hsapiens.ucsc.hg19.knowngene seqlevels bugs

updated 8.9 years ago by Hervé Pagès 16k • written 8.9 years ago by wcstcyx ▴ 30

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1.8k

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txdb threeutrsbytranscript seqlevelsstyle seqlevels

10.1 years ago Robert K. Bradley ▴ 40

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8.4k

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granges seqlevels

10.5 years ago Hermann Norpois ▴ 170

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2.2k

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variantannotation seqlevels error

updated 11.1 years ago by Valerie Obenchain ★ 6.8k • written 11.1 years ago by Asma rabe ▴ 290

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Comment: "Watched Tags" are being erased rather than updated by shepherl 4.2k

I can reproduce this and have opened an issue on the code base https://github.com/Bioconductor/support.bioconductor.org/issues/112

Comment: "Watched Tags" are being erased rather than updated by shepherl 4.2k

we can investigate this issue. thank you for bringing it to our attention

Comment: deseq2 filter the low counts by Michael Love 43k

> But within each comparison (contrast), if I trace some DEGs back to the original salmon merged gene counts (or even to normalised counts)…

Comment: deseq2 filter the low counts by empty_mt • 0

Thank you for you suggestion to look at the pre-filtering section in the DESeq2 vignettes - am I missing something? I have 6 treatments, …

Comment: deseq2 filter the low counts by Michael Love 43k

Have you seen this part: https://bioconductor.org/packages/release/bioc/vignettes/DESeq2/inst/doc/DESeq2.html#pre-filtering

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Bioconductor 3.22 Released!

Comment: "Watched Tags" are being erased rather than updated

Comment: deseq2 filter the low counts

Answer: DESeq2 interactions

Answer: Important: Bioconductor Release 3.22 Delayed

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