User: rbronste

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rbronste60
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@RBronshteyn
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Posts by rbronste

<prev • 137 results • page 1 of 14 • next >
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Plotting motif enrichment vs background - Jaspar core vertebrates
... Just thinking about different ways one could visually represent motif enrichment in target peak set over control, with significant points on the plot being marked with motif PWMs, if anyone can point me to a publication or some interesting code it would be much appreciated. Thank you! ...
jaspar meme pwm motifs motif analysis written 7 months ago by rbronste60
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Comment: C: High normalized counts on DESeq2 MAplot
... Yes I apologize did not do a simple subset operation there prior to plot.  ...
written 8 months ago by rbronste60
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Comment: C: High normalized counts on DESeq2 MAplot
... Thanks for the help. ...
written 8 months ago by rbronste60
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Comment: C: High normalized counts on DESeq2 MAplot
... Very helpful however still confused about the following: When I do: plot(log10(res$baseMean), res$log2FoldChange) ​I get now an MA plot that looks like before where every point is a black hollow circle, and if I try to limit it in this way: plot(log10(res$baseMean > 3), res$log2FoldChange & ...
written 8 months ago by rbronste60
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Comment: C: High normalized counts on DESeq2 MAplot
... Actually I would like to do both.  ...
written 8 months ago by rbronste60
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High normalized counts on DESeq2 MAplot
... I am wondering how to isolate points on an MAplot that are in the area of high normalized counts above a certain lfc threshold, without changing the low end of the normalized counts that are part of the dds. Also is there a quick way to infer at what alpha these points lie. Currently Im running the ...
deseq2 maplot written 8 months ago by rbronste60 • updated 8 months ago by James W. MacDonald50k
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Converting DESeq2 results to DiffBind object
... I was wondering whether there was a way to take DESeq2 results and convert these to a DiffBind object for downstream processing? Thanks. ...
diffbind deseq2 written 8 months ago by rbronste60
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Comment: C: Split AME .tsv file into GRanges object or DataFrame
... So after read.table, if I do as you suggest I get the following error: > gr<- GRanges(t$seq_ID) Error in .from_character_to_GRanges(from) : The character vector to convert to a GRanges object must contain strings of the form "chr:start-end" or "chr:start-end:strand", with end >=start - 1 ...
written 8 months ago by rbronste60
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Split AME .tsv file into GRanges object or DataFrame
... I have an AME motif calling output as follows (in a .tsv file) and can import this into R using read.table, however I would like to take the motif_ID, seq_ID, and class fields and split it off into a GRanges object or DataFrame, how can I go about doing this? Thanks! motif_DB ...
granges motif meme dataframe ame written 8 months ago by rbronste60 • updated 8 months ago by Michael Lawrence11k
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Comment: C: DESeq2 memory allocation question
... > sessionInfo() R version 3.4.1 (2017-06-30) Platform: x86_64-apple-darwin15.6.0 (64-bit) Running under: macOS Sierra 10.12.5 Matrix products: default BLAS: /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib LAPACK: /Library/Framework ...
written 9 months ago by rbronste60

Latest awards to rbronste

Popular Question 8 months ago, created a question with more than 1,000 views. For DiffBind BED output with score
Centurion 2.1 years ago, created 100 posts.
Supporter 2.1 years ago, voted at least 25 times.

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