User: cannin

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cannin230
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Posts by cannin

<prev • 21 results • page 1 of 3 • next >
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Answer: A: cpath is not available for cytoscape?
... The last versions of the old PC plugins for Cytoscape 2.8 are still available here: https://sourceforge.net/projects/biopax/files/other/cytoscape2_plugins/ The new one (which is called not plugin but app), for Cytoscape 3 is called CyPath2 and available in the Cytoscape Apps Store. ...
written 12 weeks ago by cannin230
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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 8 months 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 13 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 13 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 14 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 16 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 18 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 18 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 23 months ago by cannin230
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Comment: C: Finding all pathways for a gene.
... I have now updated the example ...
written 2.0 years ago by cannin230

Latest awards to cannin

Popular Question 8 months ago, created a question with more than 1,000 views. For PaxtoolsR: Aggregated Pathway Data for R
Scholar 16 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 16 months ago, created an answer with at least 3 up-votes. For A: Adding gene diagram to output from snp.plotter
Scholar 18 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 3.6 years ago, created a post with more than 5 votes. For PaxtoolsR: Aggregated Pathway Data for R

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