Bioconductor Linux

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14 results • Page 1 of 1

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Comment: limma::voom vs edgeR::voomLmFit - when to use? by Gordon Smyth 52k

voomLmFit() is in edgeR instead of limma because it needs to call edgeR::glmFit() internally to determine which of the zero observations al…

Comment: limma::voom vs edgeR::voomLmFit - when to use? by Geoff • 0

Just wondering--why was this function put into `edgeR` rather than `limma`? Maybe a bit technical, but it is a little confusing from an out…

Comment: cannot download atena annotation for human by Davide • 0

Hi Robert, I was able to solve the problem. Indeed, it stems from the co-occurrence of two different AnnotationHub available for hg38. …

Comment: Setting ylims in bam coverage plot and assigning compound sashimi numbers to ove by macdonaldfrench7286566 • 0

Regarding the ylim for the coverage [space waves][1], have you tried accessing the ylim slot of the CoverageTrack object after you've creat…

Comment: How to left_join a tidySummarizedExperiment with a GRanges object by seqnames an by Kateřina • 0

I unfortunately haven't. Non-tidy grammar is fine, but I have wanted to use tidy-only grammar. Thank you nonetheless!

Votes

Answer: parameters of filterByExpr

Answer: DESeq2 Apeglm Coefficient Reordering / Log2FoldChange Comparison Change

Answer: GAlignments Cigar to GRanges

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