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biovizBase biovi

updated 3 months ago by James W. MacDonald 64k • written 3 months ago by bernatgel ▴ 150

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Comment: rDGIdb package inconsistency with web interface by christopherjamessteel1990 • 0

That is strange as I only see that previous version message when I go on the https://beta.dgidb.org/api version. I did contact the writer …

Comment: Small RNA-seq Analysis DESEQ2 : Unexpected Significance by ATpoint ★ 3.6k

"Raw" counts, so you're plotting un-normalized data, hence plots have no meaning in terms of groupwise comparisons. Use the `normTransform`…

Answer: In DiffBind, dba.blacklist changes the minOverlap parameter by Sam ▴ 10

I have found a workaround : running dba.blacklist **after** running dba.count (while running dba.count with minOverlap=1). ``` dbObj_co…

Comment: Small RNA-seq Analysis DESEQ2 : Unexpected Significance by samer • 0

By applying the log2 transformation to the raw counts of small RNAS AND after adding 1 to each count, the resulting values often approximat…

Comment: Small RNA-seq Analysis DESEQ2 : Unexpected Significance by samer • 0

and sometimes in other count plots we observe a difference between the counts of the 2 conditions (ON/OFF) where it should be significant b…

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Answer: WGCNA documentation not available

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