User: Thomas Girke

gravatar for Thomas Girke
Thomas Girke1.7k
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United States
Website:
http://girke.bioinform...
Last seen:
2 days, 1 hour ago
Joined:
14 years, 4 months ago
Email:
t***********@ucr.edu

Posts by Thomas Girke

<prev • 186 results • page 1 of 19 • next >
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Answer: A: Bioactivity assay DBs for cheminfo packages
... A very useful resource for bioactivity data is ChEMBL. This includes many bioassays from PubChem but better curated. Their SQLite version here: ftp://ftp.ebi.ac.uk/pub/databases/chembl/ChEMBLdb/latest/ can be easily accessed from within R (e.g using RSQLite). Detailed documentation on their database ...
written 5 days ago by Thomas Girke1.7k
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Comment: C: How to remove HCL mols in Chemminer
... I will add this to the to-do list and report back when it is available. ...
written 17 days ago by Thomas Girke1.7k
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Answer: A: How to remove HCL mols in Chemminer
... Dear Anthony, Such a feature isn't currently available, at least not out of the box. Since it sounds useful, we could add it to our to-do list and let you know once it becomes available. What could help is sending me an example of a few SDFs containing the HCl contaminations you would like to remov ...
written 18 days ago by Thomas Girke1.7k
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Job: Postdoctoral positions in drug discovery and genome data science
... ## Background Two postdoctoral positions are immediately available at the University of California, Riverside to work on the integrative analysis of large-scale small molecule bioactivity data and a wide range of genome-wide profiling data. The goal of this project is to identify systems-level insig ...
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Comment: C: runCommandline error - bash: module: command not found
... Could you please provide the command(s) that you use to generate the args object that is used by runCommandline. In addition, please provide the output of sessionInfo() executed in an R session right after the error occurred.   Thomas ...
written 5 months ago by Thomas Girke1.7k
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Comment: C: Problem running (loading) systemPipeR package after downloading
... Please make sure you are installing Bioc packages, including systemPipeR, as outlined here: https://bioconductor.org/install/. Also make sure you have a recent R version installed >=3.5.0. ...
written 6 months ago by Thomas Girke1.7k
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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 12 months ago by Thomas Girke1.7k
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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 18 months ago by Thomas Girke1.7k
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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 21 months ago by Thomas Girke1.7k

Latest awards to Thomas Girke

Popular Question 5 months ago, created a question with more than 1,000 views. For Feature types in TxDb objects
Popular Question 6 months ago, created a question with more than 1,000 views. For multiple feature/mode counting with summarizeOverlaps
Scholar 2.9 years ago, created an answer that has been accepted. For A: SystemPipeR: alignments with ambiguous pairing were dumped.
Teacher 2.9 years ago, created an answer with at least 3 up-votes. For A: heatmap.2() get matrix after hierarchical clustering
Good Answer 2.9 years ago, created an answer that was upvoted at least 5 times. For A: heatmap.2() get matrix after hierarchical clustering
Appreciated 2.9 years ago, created a post with more than 5 votes. For A: heatmap.2() get matrix after hierarchical clustering
Scholar 3.4 years ago, created an answer that has been accepted. For A: Extract three types of intergenic regions
Scholar 3.4 years ago, created an answer that has been accepted. For A: Extract three types of intergenic regions
Student 3.9 years ago, asked a question with at least 3 up-votes. For Feature types in TxDb objects
Centurion 4.9 years ago, created 100 posts.

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