User: rbronste

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rbronste60
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@RBronshteyn
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Posts by rbronste

<prev • 146 results • page 1 of 15 • next >
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Comment: C: Label points on DESeq2 MA plot with interval list
... Thanks for the info Michael, my situation is actually much simpler than that since Im using DESeq2 to look for differential peaks in ChIP-seq data, so basically I am interested in taking some differential peak calls from one dataset and mapping it onto the MAplot of another, to see overlap in that f ...
written 4 weeks ago by rbronste60
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Label points on DESeq2 MA plot with interval list
... I am wondering whether it is possible to label/color individual points on a DESeq2 MA plot based on a list of intervals? Thanks. ...
annotation deseq2 maplot written 4 weeks ago by rbronste60 • updated 4 weeks ago by Michael Love26k
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diffBind volcano plot error
... Hi I am getting the following error: dba.plotVolcano(CR_count,th=0.1,fold=1,method = DBA_DESEQ2_BLOCK, bFlip = TRUE) Error in `.rowNamesDF<-`(x, value = value) : invalid 'row.names' length This happens only when I take a .csv sample file and make a secondary file with half of the condit ...
diffbind software error volcano plot written 4 weeks ago by rbronste60
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Comment: C: write.table of DESeq2 results broken down by LFC
... Any thoughts on an easy way to approach this or should I just always split the res? Thanks! ...
written 7 weeks ago by rbronste60
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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 8 weeks 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 8 weeks ago by rbronste60 • updated 8 weeks ago by Michael Love26k
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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 9 weeks ago by rbronste60 • updated 7 weeks ago by Rory Stark3.0k
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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 9 weeks 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 9 weeks ago by rbronste60 • updated 7 weeks ago by Rory Stark3.0k
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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 12 months ago by rbronste60

Latest awards to rbronste

Popular Question 11 months ago, created a question with more than 1,000 views. For DiffBind for open chromatin mapping
Popular Question 13 months ago, created a question with more than 1,000 views. For DiffBind BED output with score
Centurion 2.5 years ago, created 100 posts.
Supporter 2.5 years ago, voted at least 25 times.

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