Bioconductor Recountworkflow

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recount recountWorkflow recount3

updated 12 months ago by Leonardo Collado Torres ★ 1.0k • written 16 months ago by dml • 0

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recountWorkflow recount3

updated 15 months ago by Leonardo Collado Torres ★ 1.0k • written 16 months ago by soever ▴ 20

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recount recountWorkflow recount3

updated 12 months ago by Leonardo Collado Torres ★ 1.0k • written 17 months ago by Max Bone • 0

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recount3 recountWorkflow

updated 2.5 years ago by Leonardo Collado Torres ★ 1.0k • written 2.6 years ago by António Miguel de Jesus Domingues ▴ 510

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Comment: Differences in differential analysis methods for RNA-Seq by ATpoint ★ 4.1k

MAGeCK is a command line tool that is easy to use. I recommend you use it because a) the logFCs from DESeq2 and MAGeCK will be very similar…

Comment: Get genomic coordinates of CpGs sites (chromosomes, genomic position) by Yveto • 0

Thank for your response. It is Illumina 450 K. I use this code ```{r } library(IlluminaHumanMethylation450kanno.ilmn12.hg19) annotat…

Answer: More regions in union when increasing DBA$config$mergeOverlap by Rory Stark ★ 5.2k

I think the documentation is out of sync with the code. Positive values represent gaps between intervals and negative values represent how …

Comment: log2FoldChange value is way too different when compared with counts(dds) by Michael Love 41k

But just to be clear, this is not the same as regressing out batch from the VST (approx log transformed): ``` limma::removeBatchEffect(cou…

Comment: log2FoldChange value is way too different when compared with counts(dds) by HAK • 0

Thank you for the explanation, probably my brain just needed to accumulate enough info to understand what you are saying, but I finally got…

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A: Error in DESeqDataSet : some values in assay are not integers

Bioconductor 3.19 is Released!

Answer: DEseq2 coefficient

SPIA plotP giving error

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