User: Brian Herb

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Brian Herb80
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3 years, 4 months ago
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9 years, 2 months ago
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b********@jhmi.edu

Posts by Brian Herb

<prev • 8 results • page 1 of 1 • next >
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Comment: C: BSgenome
... And there is this for your build: http://hgdownload.soe.ucsc.edu/goldenPath/hg19/chromosomes/ On Mon, Jul 14, 2014 at 10:06 AM, James W. MacDonald wrote: > This may help clear things up for you: > > http://genome.ucsc.edu/FAQ/FAQdownloads.html#download9 > > Best, > > Jim ...
written 3.4 years ago by Brian Herb80
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Comment: C: Looping over entries of a GRanges object
... Hi Julian, I believe that some of the functions can be applied to the entire GRanges object without looping. For example you can try getSeq(BSgenome_object,GRanges_object) and this will output the sequences for each region of interest. Hopefully this still works, it has been a while since I have tr ...
written 3.5 years ago by Brian Herb80
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Job: Bioinformatics Analyst at Johns Hopkins Medical School (Masters or Ph.D.)
... The Center for Epigenetics is looking for a bioinformatics analyst with a masters or Ph.D. degree in bioinformatics or related computational fields to process genomic sequencing data and contribute novel analysis of this data in a highly collaborative environment. The biologists and statisticians of ...
sequencing epigenetics process written 3.6 years ago by Brian Herb80
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Comment: C: matchTable for pairwiseAlignment in Biostrings?
... Hi Valerie, Thank you for looking into this! I actually didn't see my post show up so I did a little more tinkering and came up with the following function, see what you think: (input is PairwiseAlignmentsSingleSubject) matchTable <- function(pwa) { p.start <- start(pattern(pwa)) p.end < ...
written 4.2 years ago by Brian Herb80
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matchTable for pairwiseAlignment in Biostrings?
... Hi all, I feel like I'm missing some obvious function, but is there a simple way to output a table of matching start and end positions between the subject and pattern in a pairwiseAlignment result (say from a global-local alignment)? For example: s.pos1 s.pos2 p.pos1 p.pos2 [1,] 354 359 ...
written 4.2 years ago by Brian Herb80 • updated 4.2 years ago by Valerie Obenchain ♦♦ 6.4k
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Comment: C: Question about interpretation of CHARM results
... Zeynep- You also mentioned that you are using MeDip arrays, and if that also means that you used the MeDip protocol to fractionate your DNA, keep in mind that the CHARM package is written with the assumption that the restriction enzyme McrBC is used to fractionate the DNA into total and unmethylate ...
written 5.3 years ago by Brian Herb80
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Answer: A: Basic R question
... Nathalie- try- chr1=subset(object,object$chrom==1) where object is your dataframe On Thu, Jul 14, 2011 at 10:34 AM, Nathalie Conte wrote: > HI , > I want to subset a list I have in order to look only the data from chosen > chromosomes. > my file is this format ( see attached for a ...
written 6.4 years ago by Brian Herb80
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problem with makePDpackage, geometry issue
... I'm running into a small problem creating the PD package for the bee. It is looking for geometry info, but I can't seem to add it. The package is created with no error, and the XYS files seem to load, but returns: Error in geometry(get(pkgname)) : no slot of name "geometry" for this object of clas ...
preprocessing probe written 9.2 years ago by Brian Herb80

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