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Comment: Suggested package missing from Development version of Bioconductor
by
Richard
• 0
I have just contacted the maintainer. Is it okay if I leave the package in Suggests for now and then remove it before the next Bioconductor…
Answer: shinyMethyl - saving the file
by
Guillaume Devailly
▴ 60
You can probably save individual plots by right-clicking on them an save individual images. Maybe printing the page as a pdf will also work…
Answer: Deseq2 calculated log2foldchange not consistent with RPM in IP-small RNA-seq
by
Michael Love
40k
Did you manually calculate RPMs? Try `fpm(dds)` for comparison, as this also uses DESeq2 median ratio scaling.
Comment: collapseReplicates error after tximeta
by
Michael Love
40k
A note: I've now changed collapseReplicates() to output a loud warning when it is run on a DESeqDataSet (SummarizedExperiment) with more th…
Comment: Suggested package missing from Development version of Bioconductor
by
shepherl
3.5k
Have you tried reaching out to the maintainers? If they do not fix the package it will remain unavailable and cause ERROR in your package.…
Votes
DESeq2 analysis with only two replicates
Comment: Batch correction and repeated measures
batch effect : comBat or blocking in limma ?
Batch correction and repeated measures
Comment: Does countsFromAbundance="lengthScaledTPM" produce un-normalized counts?
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