User: cannin

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cannin230
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2 months ago
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3 years, 2 months ago
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Posts by cannin

<prev • 20 results • page 1 of 2 • next >
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Answer: A: How to obtain DrugBank Drug Name and SMILES Data from DrugBank ID?
... Try the PUG PubChem API: `https://pubchem.ncbi.nlm.nih.gov/pug_rest/PUG_REST.html` Using Topotecan (DB01030) as an example below: Get data by DrugBank ID: `https://pubchem.ncbi.nlm.nih.gov/rest/pug/substance/sourceid/drugbank/DB01030/XML` This XML has a PubChem Compound ID, look for: `60700` Th ...
written 9 weeks ago by cannin230
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Answer: A: How to plot schematic diagram of the pathway?
... Here is a tool in development by the group of Ugur Dogrusoz at Bilkent University and colleagues to let you create the pathway diagrams. http://pathwaymapper.org/ Many of the existing TCGA diagrams have been reproduced and you can overlay TCGA alteration data from cBioPortal using the site. At ...
written 6 months ago by cannin230
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Answer: A: Using BioPAX & associated tools
... * Databases like KEGG and Reactome already exist in Pathway Commons, so you might not need to import anything: http://www.pathwaycommons.org/pc2/ If you need to do custom imports, take a look at this repository, it might help: https://bitbucket.org/armish/gsoc14/ * paxtoolsr uses the Java Paxtools ...
written 7 months ago by cannin230
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Answer: A: NCI-60 dataset in R
... Use the rcellminer package. https://bioconductor.org/packages/release/bioc/html/rcellminer.html https://www.ncbi.nlm.nih.gov/pubmed/26635141 Those R scripts that you're about to write if you download the data directly and import have been written (and tested) for you by the CellMiner group and co ...
written 8 months ago by cannin230
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Answer: A: Adding gene diagram to output from snp.plotter
... You're correct. snp.plotter does not include a feature to incorporate the LocusZoom plots. Likely, the authors of the article created the two plots and then combined them in Illustrator or Inkscape. snp.plotter can produce PDFs so you would not lose quality by combining the images. ...
written 9 months ago by cannin230
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Comment: C: Extract all the information of a pathway from a Biopax lv2 or 3 file
... Try this to change the available memory limit in paxtoolsr: http://bioconductor.org/packages/release/bioc/vignettes/paxtoolsr/inst/doc/using_paxtoolsr.html#memory-limits-specify-jvm-maximum-heap-size ...
written 12 months ago by cannin230
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Answer: A: Extract all the information of a pathway from a Biopax lv2 or 3 file
... Try this just using paxtoolsr with the BioPAX Level 3 file you have: # Update paxtoolsr First, update to the paxtoolsr development version (I just updated a few things): setRepositories(ind=1:6) options(repos="http://cran.rstudio.com/") if(!require(devtools)) { install.packages("devto ...
written 12 months ago by cannin230
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Comment: C: How to combine a different sources of pathway database (KEGG, BioCarta) for Path
... If you get [paxtoolsr][1] installed you can grab all the gene sets provided by [Pathway Commons][2] by running this command: geneSets <- downloadPc2("PathwayCommons.8.All.GSEA.hgnc.gmt.gz", version="8") as a list of vectors. You'll likely want to filter out pathways thas have one or few ge ...
written 17 months ago by cannin230
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Comment: C: Finding all pathways for a gene.
... I have now updated the example ...
written 18 months ago by cannin230
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Comment: C: Finding all pathways for a gene.
... You'll need to update the PaxtoolsR package; there was recent reorganization of data that is caused the issue. Check this [issue](https://github.com/BioPAX/paxtoolsr/issues/2) in the code repository for more information. ...
written 18 months ago by cannin230

Latest awards to cannin

Scholar 9 months ago, created an answer that has been accepted. For A: Extract all the information of a pathway from a Biopax lv2 or 3 file
Teacher 9 months ago, created an answer with at least 3 up-votes. For A: Adding gene diagram to output from snp.plotter
Scholar 12 months ago, created an answer that has been accepted. For A: Extract all the information of a pathway from a Biopax lv2 or 3 file
Appreciated 3.0 years ago, created a post with more than 5 votes. For PaxtoolsR: Aggregated Pathway Data for R

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