User: cannin

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cannin250
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Posts by cannin

<prev • 24 results • page 1 of 3 • next >
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Comment: C: NCI-60 dataset in R
... Not at the moment; you'll need to contact: Webadmin@discover.nci.nih.gov ...
written 5 months ago by cannin250
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Answer: A: Convert KEGG KGML files in GPML format
... A less obvious route, but it might get you to what you want: SBGN and SBGNML were meant as exchange formats for pathway diagrams: Software support for SBGN maps: SBGN-ML and LibSBGN. https://www.ncbi.nlm.nih.gov/pubmed/22581176 The Pathway Commons database aggregates from many sources, includin ...
written 5 months ago by cannin250
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Answer: A: Comparing NCI-60 transcriptome with another variable to determine genes that cor
... You can use the rcellminer R package: http://bioconductor.org/packages/release/bioc/vignettes/rcellminer/inst/doc/rcellminerUsage.html#correlating-dna-copy-number-alteration-and-gene-expression to quickly identify genes of interest that match a pattern of interest in the NCI-60. Separately, the ...
written 10 months ago by cannin250
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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 20 months ago by cannin250
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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 2.1 years ago by cannin250
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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 2.5 years ago by cannin250
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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 2.5 years ago by cannin250
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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 2.6 years ago by cannin250
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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 2.7 years ago by cannin250
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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 2.9 years ago by cannin250

Latest awards to cannin

Popular Question 7 months ago, created a question with more than 1,000 views. For PaxtoolsR: Aggregated Pathway Data for R
Scholar 10 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
Popular Question 2.1 years ago, created a question with more than 1,000 views. For PaxtoolsR: Aggregated Pathway Data for R
Scholar 2.7 years 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 2.7 years ago, created an answer with at least 3 up-votes. For A: Adding gene diagram to output from snp.plotter
Scholar 2.9 years 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 5.0 years ago, created a post with more than 5 votes. For PaxtoolsR: Aggregated Pathway Data for R

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