User: bmreilly

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bmreilly0
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Posts by bmreilly

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Comment: C: How to link methylation code from UCSC (hg19-cg07790169) to ENSEMBL genome code
... Dusan, see my comment above on James' post.  There are R packages which you will likely find useful for analyzing 450k data.  See 'missMethyl' . ...
written 10 weeks ago by bmreilly0
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Comment: C: How to link methylation code from UCSC (hg19-cg07790169) to ENSEMBL genome code
... James, there is some literature on using goseq for DNA methylation data, and there is in fact a Bioconductor package called 'missMethyl' which has a function called 'gometh' which was specifically developed to apply goseq methods to the illumina 450k platform.  The idea being that genes with differi ...
written 10 weeks ago by bmreilly0
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Comment: C: Cannot get ggbio autoplot to run successfully on R 3.2 (3.2.2 or 3.2.3)
... I just updated to bioConductor 3.2 and I am getting the exact same error.... I have R version 3.2.3 though, do you think that may have anything to do with it? ...
written 2.4 years ago by bmreilly0
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Comment: C: RnBeads cannot locate libjasper.so.1
... It turns out the problem was in fact due to the Jasper-libs package not being installed on the compute nodes I was using.  I am new to using the shared computing cluster, so I was not aware of the possibility that the compute nodes would have different software than the nodes where I was setting up ...
written 3.0 years ago by bmreilly0
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RnBeads cannot locate libjasper.so.1
... I am attempting to run RnBeads on my institutions Cluster, and I keep getting stuck at the same step yielding this error: Loading required package: doParallel /usr/bin/gs: error while loading shared libraries: libjasper.so.1: cannot open shared object file: No such file or directory Error in logge ...
rnbeads cluster gs ghostscript shared libraries written 3.0 years ago by bmreilly0
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Comment: C: Package RnBeads not available for R 3.1.2?
... Great, thanks for the tip! ...
written 3.0 years ago by bmreilly0
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Comment: C: Package RnBeads not available for R 3.1.2?
... Okay, thanks for pointing that out.  Was I misinterpreting the dependencies table on the landing page?  Why does the dependencies table show that RnBeads depends on =>R-3.0.0 when it will only run on 3.2?  Should I just infer the R version based on the BIoconductor version in the future? ...
written 3.0 years ago by bmreilly0
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Package RnBeads not available for R 3.1.2?
... I am having trouble installing the package 'RnBeads' on my institutions cluster. The cluster is running R version 3.1.2. and Bioconductor 3.0, BiocInstaller 1.16.5. when I do: source("http://bioconductor.org/biocLite.R") biocLite("RnBeads") I keep getting the error: Warning message: package ...
packages rnbeads r 3.1.2 written 3.0 years ago by bmreilly0

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Popular Question 14 months ago, created a question with more than 1,000 views. For RnBeads cannot locate libjasper.so.1

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