Bioconductor Co-expression

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biologicalnetworkanalysis genomes RNA-Seq co-expression wgcna

13 months ago Fernanda • 0

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1.2k

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network co-expression WGCNA

updated 3.1 years ago by andres.firrincieli ▴ 50 • written 3.1 years ago by ikumar2000 ▴ 10

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1.2k

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wgcna co-expression

updated 6.2 years ago by mikhael.manurung ▴ 280 • written 6.3 years ago by Lin ▴ 50

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1.4k

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wgcna network co-expression rnaseq

updated 6.5 years ago by Peter Langfelder ★ 3.0k • written 6.5 years ago by Arindam ▴ 80

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6.1k

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WGCNA R network co-expression

updated 2.8 years ago by Peter Langfelder ★ 3.0k • written 6.5 years ago by avelarbio46 ▴ 10

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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: deseq2 filter the low counts

Answer: DESeq2 interactions

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