User: Thomas Girke

gravatar for Thomas Girke
Thomas Girke1.6k
Reputation:
1,650
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Location:
United States
Website:
http://girke.bioinform...
Last seen:
5 months ago
Joined:
13 years, 9 months ago
Email:
t***********@ucr.edu

Posts by Thomas Girke

<prev • 180 results • page 1 of 18 • next >
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Answer: A: How do I convert kegg info on drug to a format allowing me to calculate similari
... Many options exist to address this need. Here are just a few using your specific example: https://gist.github.com/tgirke/fb4d7ab4cc555968b521f4d8e624cd79. Thomas ...
written 5 months ago by Thomas Girke1.6k
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Answer: A: What R version does systemPipeR runs
... The package was released in fall 2014 (R/3.1.x and Bioc/3.0). So it should be available under R/3.2.5 as well as the latest R version 3.4.x. BatchJobs (CRAN package) should also be available for the R versions you are mentioning as well as the latest one (see here). If the install isn't working for ...
written 11 months ago by Thomas Girke1.6k
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Job: Postdoc Position in Genome Data Science
... Background The Girke group has an opening for a postdoctoral researcher. This position is about the development of integrative analysis methods for multidimensional data sets from a variety of next generation sequencing (NGS) technologies and their implementation in form of R/Bioconductor packages.  ...
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Answer: A: drawing chemical from smile 2D/3D
... The online structure viewing via sdf.visualize() is working again. The server needed a restart. Thanks for letting us know. Please note, the structure rendering functionalities in ChemmineR and the affiliated online service are for 2D encodings, 3D representations are not expected to look good. If ...
written 14 months ago by Thomas Girke1.6k
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Comment: C: output of propOB function ChemmineR
... Dear Elisa, This might be an oversight updating the help file. I let Kevin Horan comment on this.  Are there specific descriptors you are interested in? As you know there are hundreds of them and propOB just generates a few common ones. With ChemmineR itself you can also generate quite few that co ...
written 17 months ago by Thomas Girke1.6k
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Answer: A: SystemPipeR: alignments with ambiguous pairing were dumped.
... Dear Abass,  What makes you believe that an alignment rate around 90% is low? Especially, for PE reads this is reasonable. Even 70% is not too bad. You could certainly try to diagnose the source of this drop for some of your samples (e.g. lower quality, adapter contaminations, PCR artifacts, etc). ...
written 21 months ago by Thomas Girke1.6k
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Answer: A: Problem with systemPipeR package: run_edgeR or run_DESeq2 functions don't work
... Yes, most likely something is wrong with your count object (countDF) and/or targets file. BTW, if you just want to run the GO analysis then all you need is a list containing character vectors of gene set labels and each list component has some name meaningful to you.  To identify the source of your ...
written 22 months ago by Thomas Girke1.6k
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Job: Postdoc Position in Computational Biology
... Background This postdoctoral position is about the development of analysis methods for multidimensional data sets from high-throughput technologies combining chemical genomics and various applications of next generation sequencing (NGS) technologies. It includes both discovery-oriented data analysi ...
job bioinformatician job written 24 months ago by Thomas Girke1.6k
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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 2.0 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 2.1 years ago by Thomas Girke1.6k

Latest awards to Thomas Girke

Appreciated 2.3 years ago, created a post with more than 5 votes. For A: heatmap.2() get matrix after hierarchical clustering
Teacher 2.3 years ago, created an answer with at least 3 up-votes. For A: heatmap.2() get matrix after hierarchical clustering
Scholar 2.3 years ago, created an answer that has been accepted. For A: SystemPipeR: alignments with ambiguous pairing were dumped.
Good Answer 2.3 years ago, created an answer that was upvoted at least 5 times. For A: heatmap.2() get matrix after hierarchical clustering
Scholar 2.8 years ago, created an answer that has been accepted. For A: Extract three types of intergenic regions
Scholar 2.8 years ago, created an answer that has been accepted. For A: Extract three types of intergenic regions
Student 3.4 years ago, asked a question with at least 3 up-votes. For Feature types in TxDb objects
Centurion 4.3 years ago, created 100 posts.

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