User: Thomas Girke

gravatar for Thomas Girke
Thomas Girke1.6k
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Website:
http://girke.bioinform...
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Joined:
13 years, 11 months ago
Email:
t***********@ucr.edu

Posts by Thomas Girke

<prev • 182 results • page 2 of 19 • next >
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Comment: C: Appeal to DESeq2 authors: please keep results reproducible across version
... Managing software versions under a simple module system (environment modules) can be a great help here especially on shared research computing systems. This way you can always choose between current and historical versions whether this is R or most other software.  ...
written 2.2 years ago by Thomas Girke1.6k
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Comment: C: ERROR: dependency 'GO.db' is not available for package 'systemPipeR'
... RStudio crashes as a result of resizing the plotting window are not uncommon. As shown in the vignette(s), redirecting the seeFastq output to image files with pdf() or png() rather than viewing them in RStudio is highly recommended since those plots can get really large, especially if you want to co ...
written 2.2 years ago by Thomas Girke1.6k
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Comment: C: ERROR: dependency 'GO.db' is not available for package 'systemPipeR'
... I recommend working through the main manual (HTML Overview Vignette here) first which explains the overall concepts of the workflows and the expected directory structure.  The additional subdirectory you mention above is generated by genWorkenvir() on Windows only. I definitely will fix this incons ...
written 2.2 years ago by Thomas Girke1.6k
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Answer: A: ERROR: dependency 'GO.db' is not available for package 'systemPipeR'
... Sorry about the frustration, but this will all go away if you can fix your R/Bioc install. In a functional environment, biocLite() will install all dependency package for you automatically and you only need to do this once. On Windows (and OS X) these installs are also very fast since pre-compiled b ...
written 2.2 years ago by Thomas Girke1.6k
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Answer: A: ERROR: dependency 'GO.db' is not available for package 'systemPipeR'
... You need to fix your R installation or nothing will work. Getting admin permissions for the system you are on may simplify this task.    ...
written 2.2 years ago by Thomas Girke1.6k
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Answer: A: ERROR: dependency 'GO.db' is not available for package 'systemPipeR'
... A few suggestions. First, you want to resolve your permission issue on your system for installing packages (e.g. run with admin permissions). After this please install systemPipeR like any other Bioconductor package with: source("https://bioconductor.org/biocLite.R") biocLite("systemPipeR") A few ...
written 2.2 years ago by Thomas Girke1.6k
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Comment: C: SystemPipeR GO term enrichment analysis - filterDEG
... You are not saying what your cutoff for the adjusted p-value was. Note, for GO:0006954 the adjusted p-value is barely significant. Minor changes in the enrichment may bring it above the cutoff you are using, so I wouldn't be surprised if any subset of up_down was dropped in the result. If you want t ...
written 2.4 years ago by Thomas Girke1.6k
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Answer: A: SystemPipeR GO term enrichment analysis - filterDEG
... This could happen when a gene set is smaller than the minimum number defined under the CLSZ argument of the GOCluster_Report function, or the enrichment p-value for a GO node does not meet the threshold requirement defined under cutoff. Note, this function knows nothing about the nature or source of ...
written 2.4 years ago by Thomas Girke1.6k
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Answer: A: Error during installation of ChemmineOB R package
... The header files might be missing in your install of OpenBabel. On Ubuntu you want to install OpenBabel like this:  sudo apt-get install libopenbabel-dev After this, try to install ChemmineOB from R with biocLite(...) or the command-line. More detail on debugging Linux installs are provided in t ...
written 2.4 years ago by Thomas Girke1.6k
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Answer: A: ChemmineR package - fpSim and cmp.similarity - Tanimoto kernels
... For fingerprints you use fpSim. The cmp.similarity function has been designed for atom pairs which are integer vectors of variable length while fingerprints are binary representations of fixed length. A special case would be atom pair fingerprints which are fingerprints generated from atom pairs. He ...
written 2.5 years ago by Thomas Girke1.6k

Latest awards to Thomas Girke

Popular Question 6 weeks ago, created a question with more than 1,000 views. For multiple feature/mode counting with summarizeOverlaps
Teacher 2.5 years ago, created an answer with at least 3 up-votes. For A: heatmap.2() get matrix after hierarchical clustering
Scholar 2.5 years ago, created an answer that has been accepted. For A: SystemPipeR: alignments with ambiguous pairing were dumped.
Good Answer 2.5 years ago, created an answer that was upvoted at least 5 times. For A: heatmap.2() get matrix after hierarchical clustering
Appreciated 2.5 years ago, created a post with more than 5 votes. For A: heatmap.2() get matrix after hierarchical clustering
Scholar 3.0 years ago, created an answer that has been accepted. For A: Extract three types of intergenic regions
Scholar 3.0 years ago, created an answer that has been accepted. For A: Extract three types of intergenic regions
Student 3.5 years ago, asked a question with at least 3 up-votes. For Feature types in TxDb objects
Centurion 4.4 years ago, created 100 posts.

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