User: Tengfei Yin

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Tengfei Yin420
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Posts by Tengfei Yin

<prev • 42 results • page 1 of 5 • next >
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Answer: A: color-coded arch intensity in ggbio
... do you mean something like alpha = abs(intensity)? On Wed, May 21, 2014 at 9:39 PM, Bogdan Tanasa wrote: > Dear Tengfei, greetings . > > About ggbio : please could you advise on how I could color-code some > arches based on the intensity of the interaction (arch), > > as of now ...
written 5.4 years ago by Tengfei Yin420
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Comment: C: ggbio facet_gr example sought
... Hi Michael and Malcolm, Sorry for the late reply, that's actually a bug in ggbio now. I did deprecate facet_gr() function, but the feature is kept, it is supposed (used) to work when you pass GRanges to arguments 'facets', either in autoplot() or the low level API. Some of my updates broke this fe ...
written 6.2 years ago by Tengfei Yin420
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Comment: C: about GenomicRanges keepseqlevel deprecation and ggbio
... Hi Pablo, Thanks for your feedback and sorry for the late fix, I have been busy with something else recently, but I promise I will fix ggbio in devel branch this week, and update with the new developed features. Tengfei On Mon, Jul 15, 2013 at 12:59 AM, Pablo marin-garcia < harpactocrates@gma ...
written 6.3 years ago by Tengfei Yin420
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Answer: A: status of visnab
... Hi Abhi, Thanks for your attention, if you are interested in trying visab, I fixed some bugs couple days ago in github, you can try to play with it, but it only provides a minimal bam file viewer/some infrastructures for now, examples command is here https://github.com/tengfei/visnab/blob/master/i ...
written 6.5 years ago by Tengfei Yin420
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Comment: C: Visualization of alignments with mismatch bases
... Hi Martin, thanks for your suggestion, GappedAlignments looks promising and together with MD tag as Michael suggested, I should get what I want, I will go through your source code carefully later. I tried your sample code, that actually looks pretty cool with shiny and responsive too. Is that goin ...
written 6.6 years ago by Tengfei Yin420
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Comment: C: Visualization of alignments with mismatch bases
... Michael, Thanks a lot for you suggestion, I will think about it. Tengfei On Fri, Mar 1, 2013 at 7:03 AM, Michael Lawrence wrote: > You should check out the GappedReads object from ShortRead. It extends > GappedAlignments to hold the read sequence information in a DNAStringSet. > You coul ...
written 6.6 years ago by Tengfei Yin420
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Answer: A: Visualization of alignments with mismatch bases
... On Thu, Feb 28, 2013 at 11:08 PM, Michael Lawrence < lawrence.michael@gene.com> wrote: > > > > On Thu, Feb 28, 2013 at 11:46 AM, Tengfei Yin wrote: > >> On Thu, Feb 28, 2013 at 11:46 AM, Julian Gehring >> wrote: >> >> > Hi, >> > >> > ...
written 6.6 years ago by Tengfei Yin420
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Comment: C: Visualization of alignments with mismatch bases
... Thanks Julian, for you feedback, I will keep your feature request in my mind, and will think about implementing something like different modes/types in geom_alignment or stat_mismatch function in ggbio. Tengfei On Thu, Feb 28, 2013 at 2:31 PM, Julian Gehring wrote: > Hi Tengfei, > > What ...
written 6.6 years ago by Tengfei Yin420
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Answer: A: Visualization of alignments with mismatch bases
... On Thu, Feb 28, 2013 at 11:46 AM, Julian Gehring wrote: > Hi, > > Is there a good way to visualize aligned reads with mismatch bases (SNPs) > along the genome (similar to what one knows from the standard genome > browsers)? > > 'ggbio' came to my mind with which plotting a pile ...
written 6.6 years ago by Tengfei Yin420
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Answer: A: plotting BED intervals to TSS regions
... Hi Seb, I guess before visualization you need to get the summary statistics ready first, I got one idea, maybe you could give a try, and I assume the count you want is based on a per base resolution 1. 'import' function in package rtracklayer to import your BED files and TSS files as GRanges objec ...
written 6.7 years ago by Tengfei Yin420

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