User: Joern Toedling

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50
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Last seen:
7 years, 1 month ago
Joined:
8 years, 5 months ago
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j*********@imb-mainz.de

Posts by Joern Toedling

<prev • 5 results • page 1 of 1 • next >
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Answer: A: Analysis of chIP-chip
... Hello, assuming that you are talking about the Ringo package, I am not sure which parts of the vignette you modified for your own data, but apparently you have been missing a step. In general, the data of ChIP and Input channel are read in, stored as an object of class RGList and then the function ...
written 7.2 years ago by Joern Toedling50
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Answer: A: GenomeGraphs question
... Hello, the function "setPar" might be what you are looking for. You can check the parameters associated with each object easily by just typing the object's name, such as > snpPlot and set them this way: > setPar(snpPlot, "pointSize", 2) # or something else than 2 and then calling "gdPlot ...
written 7.8 years ago by Joern Toedling50
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Fwd: Re: Installing Bioconductor packages on R 2.14.0 *without* administrator rights / from a script
... Hello, without touching upon any recent changes in biocLite, I would recommend the following simple way to install packages without administrator rights. 1. Create an environment variable called "R_LIBS" and point that a writeable directory where you want your packages to go to. For example in the ...
go written 8.0 years ago by Joern Toedling50
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Answer: A: perWindow chr coordinates (girafe)
... Hi Karl, remember that you can always check a function's source code by typing the function name without brackets. You can see that indeed the only organism-related information needed by "perWindow" are the lengths of the individual chromosomes. If there is no organism annotation-package related ...
written 8.2 years ago by Joern Toedling50
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Comment: C: a question about girafe
... Hello, note that package "girafe" also contains a function called "agiFromBam" which directly reads in sorted and indexed BAM files into an object of the AlignedGenomeIntervals class. This function also relies on functionalities of the Rsamtools package but should be faster and more memory-efficien ...
written 8.4 years ago by Joern Toedling50

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