Bioconductor Coldata

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1.1k

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DESeq2 design coldata

updated 18 months ago by swbarnes2 ★ 1.4k • written 18 months ago by arfranco ▴ 130

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1.3k

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ColData pheatmap DESeq2

written 2.4 years ago by dania.khalid • 0

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2.0k

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SingleCellExperiment colData rename

updated 2.7 years ago by Basti ▴ 780 • written 2.7 years ago by achoppe ▴ 10

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913

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BiSeq Coldata

5.4 years ago akhaira • 0

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2.2k

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deseq2 levels factor colData

updated 6.7 years ago by Michael Love 43k • written 6.7 years ago by ariel ▴ 20

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50k

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deseq2 coldata

updated 7.0 years ago by swbarnes2 ★ 1.4k • written 7.0 years ago by mjrarcher ▴ 10

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4.3k

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variantannotation coldata

updated 7.1 years ago by Valerie Obenchain ★ 6.8k • written 7.1 years ago by lvclark ▴ 10

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4.8k

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deseq2 coldata NA

updated 14 months ago by Michael Love 43k • written 7.2 years ago by t.kuilman ▴ 170

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2.0k

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multiassayexperiment colData

updated 7.9 years ago by Levi Waldron ★ 1.1k • written 7.9 years ago by Lluís Revilla Sancho ▴ 760

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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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