User: Chris Stubben

gravatar for Chris Stubben
Reputation:
40
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New User
Location:
Salt Lake City, Utah
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Google Scholar Page
Last seen:
2 months, 1 week ago
Joined:
2 years, 2 months ago
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Posts by Chris Stubben

<prev • 11 results • page 1 of 2 • next >
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Comment: C: Gviz color alignments by read strand
... That works great, thanks.  I just had to add options(ucscChromosomeNames=FALSE) ...
written 4 months ago by Chris Stubben40
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Comment: C: Gviz color alignments by read strand
... I have some Digenome-seq data and want to plot potential cut sites that should have reads stacked on opposite strands (so individual reads colored by read strand).  My code works if there's only a few hundred reads that all fit in the plot. ...
written 4 months ago by Chris Stubben40
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Comment: C: Gviz color alignments by read strand
... This only works if ALL reads are plotted in the display. ...
written 7 months ago by Chris Stubben40
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Answer: A: Gviz color alignments by read strand
... I can color by read strand if I subset a data.frame before creating the alignments track.   bam1 <- readGAlignments(BamFile(system.file(package="Gviz", "extdata", "gapped.bam"))) bamdf <- data.frame(bam1) names(bamdf)[1] <- "chromosome" bamdf <- subset(bamdf, start > 2997000 & e ...
written 7 months ago by Chris Stubben40
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Gviz color alignments by read strand
... Is there a way to use fill.reads to color alignments by read strand?  I would like to plot these on a single track library(Gviz) alTrack <- AlignmentsTrack(system.file(package="Gviz", "extdata",   "gapped.bam"), isPaired=FALSE) plotTracks(alTrack, from=2997000, to=2998200, chromosome="chr12", ...
gviz written 7 months ago by Chris Stubben40 • updated 4 months ago by Robert Ivanek590
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Comment: C: compare one group to mean of two others in DESeq2 with betaprior=FALSE
... Is there any way to shrink fold changes if you use  ~0 + trt?  With betaPrior = FALSE, I get the same error at a later step running lfcShrink(dds, contrast= c("trt", "C", "A")) ...
written 15 months ago by Chris Stubben40
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Comment: C: compare one group to mean of two others in DESeq2 with betaprior=FALSE
... Thanks, I remember reading that you should not use ~0 + trt, but that must be when betaPrior=TRUE ...
written 15 months ago by Chris Stubben40
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compare one group to mean of two others in DESeq2 with betaprior=FALSE
... Is it possible to compare one group with the mean of two others if betaPrior=FALSE?   In previous versions of DESeq2, I could group C vs A+B using a list below, but I'm not sure how to work with the new resultsNames output like trt_B_vs_A. dds <- makeExampleDESeqDataSet(n=1000, m=18) dds$trt &l ...
deseq2 written 15 months ago by Chris Stubben40 • updated 15 months ago by Michael Love23k
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Scan error using biomart with version option
... I get a scan error if I use the version option in biomaRt while running latest R version 3.4.2.    ensembl <- useEnsembl(biomart="ensembl", dataset="hsapiens_gene_ensembl", version=90) ensembl@host [1] "http://e90.ensembl.org:80/biomart/martservice" getBM(attributes=c('ensembl_gene_id','externa ...
biomart written 17 months ago by Chris Stubben40 • updated 16 months ago by Mike Smith3.5k
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Comment: C: Reordering factor levels in DESeq2 causes results error in cleanContrast
... It's not very clear in the Note on Factor Levels in the DESeq2 vignette that you should not reorder factors after running DESeq2.   I will only reorder factors in sample tables from now on. ...
written 18 months ago by Chris Stubben40

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Popular Question 13 months ago, created a question with more than 1,000 views. For Scan error using biomart with version option
Student 13 months ago, asked a question with at least 3 up-votes. For Scan error using biomart with version option

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