Bioconductor RRBSdata

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1.3k

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RRBSdata edgeR

updated 21 months ago by Gordon Smyth 53k • written 21 months ago by annasoudi • 0

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1.1k

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RRBSdata edgeR methylationArrayAnalysis

2.3 years ago Krzysztof • 0

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1.4k

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hiAnnotator bsseq DifferentialMethylation edgeR RRBSdata

3.5 years ago • updated 3.4 years ago Mageiros • 0

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2.4k

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DifferentialMethylation RRBSdata edgeR

updated 3.5 years ago by Gordon Smyth 53k • written 3.5 years ago by Mageiros • 0

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1.8k

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BatchEffect combat sva edgeR RRBSdata

updated 3.5 years ago by Gordon Smyth 53k • written 3.5 years ago by Mageiros • 0

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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

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