Bioconductor DiFFBind

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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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DiffBind

updated 10 hours ago by Rory Stark ★ 5.2k • written 1 day ago by Ian D. ▴ 70

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Comment: Deseq2 and Normalization of RNA sequencing data by ATpoint ★ 4.1k

There is no expectation of normality that is realistic in terms of expression level. Levels are widely different between genes, and counts …

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…

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Bioconductor 3.19 is Released!

Answer: DEseq2 coefficient

SPIA plotP giving error

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