Bioconductor DiFFBind

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DiffBind

updated 1 hour ago by Rory Stark ★ 5.2k • written 15 hours ago by Ian D. ▴ 70

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DiffBind ChIPSeqData DESeq2

updated 1 day ago by Michael Love 41k • written 1 day ago by marcusn • 0

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DiffBind

updated 5 days ago by ATpoint ★ 4.1k • written 7 days ago by Shloka • 0

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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…

Answer: Getting Error in hclust(d, method = method): NA/NaN/Inf in foreign function call by ATpoint ★ 4.1k

Here the error probably means that you habe genes where expression scross all samples is the same. Rowscaling is value minus mean divided b…

Comment: Store output of matchPWM() by James W. MacDonald 65k

Here's a self contained reproducible example, using part of the example in `?matchPWM` ``` > library(Biostrings) > data(HNF4alpha) > libr…

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Bioconductor 3.19 is Released!

Answer: DEseq2 coefficient

SPIA plotP giving error

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