User: rbronste

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rbronste60
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@RBronshteyn
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Posts by rbronste

<prev • 142 results • page 1 of 15 • next >
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Comment: C: write.table of DESeq2 results broken down by LFC
... I just want to export two BED files via write.table, one that has all of the > 0 LFC values and the second which has all the <0 LFC values from res ...
written 2 days ago by rbronste60
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write.table of DESeq2 results broken down by LFC
... Hi, I am writing a table of DESeq2 results in the following way and just wondering how to easily write to two separate tables based on the LFCs below: summary.DESeqResults(treatment_pw_padj.001_sorted) out of 5203 with nonzero total read count adjusted p-value < 0.1 LFC > ...
deseq2 written 2 days ago by rbronste60 • updated 2 days ago by Michael Love25k
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dba.count filter example in manual
... Hi I had a question about the following example in the diffbind tutorial: # Plot effect of a range of filter values and then apply filter data(tamoxifen_counts) rate.max <- dba.count(tamoxifen, peaks=NULL, filter=0:250) rate.sum <- dba.count(tamoxifen, peaks=NULL, filter=0:250,fi ...
diffbind written 8 days ago by rbronste60
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Comment: C: Filtering counts in SummarizedExperiment
... This isn't really a Bioconductor answer either. I apologize for the vagueness of the question but I think you know what I was asking and why I asked it here. Your response rehashed what I indicated I already understood. Thank you. ...
written 10 days ago by rbronste60
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Filtering counts in SummarizedExperiment
... Hi I am making a SummarizedExperiment from a DiffBind dba.peakset in the following way (to use in DESeq2): rangedCounts <- dba.peakset(Adult_count, bRetrieve=TRUE) nrows <- 1025488 ncols <- 8 counts <- matrix(runif(nrows * ncols, 1, 1e4), nrows) rowRanges<-GR ...
diffbind summarizedexperiment matrix rangedcounts written 11 days ago by rbronste60 • updated 10 days ago by James W. MacDonald51k
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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 10 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 11 months ago by rbronste60
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Comment: C: High normalized counts on DESeq2 MAplot
... Thanks for the help. ...
written 11 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 11 months ago by rbronste60
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Comment: C: High normalized counts on DESeq2 MAplot
... Actually I would like to do both.  ...
written 11 months ago by rbronste60

Latest awards to rbronste

Popular Question 9 months ago, created a question with more than 1,000 views. For DiffBind for open chromatin mapping
Popular Question 11 months ago, created a question with more than 1,000 views. For DiffBind BED output with score
Centurion 2.3 years ago, created 100 posts.
Supporter 2.3 years ago, voted at least 25 times.

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