User: EverInEarnest

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Posts by EverInEarnest

<prev • 18 results • page 1 of 2 • next >
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Comment: C: Retrieving age metadata for GEO samples
... Thanks for your helpful response, Sean! I will look into STARGEO to determine whether it will be helpful. I don't believe that my ~2,000 samples are clustered into only a few GEO Series records, but I'll check out your updates to how GEOquery parses the GEO GSEMatrix records. ...
written 6 months ago by EverInEarnest30
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Retrieving age metadata for GEO samples
... I have a set of ~2,000 Gene Expression Omnibus (GEO) sample names in the format GSM1234567. For each sample, I need to obtain the age-related metadata, which will include both a value or range of values (e.g. "5" or "18-24") and a unit of time (e.g. "months" or "years"). I located the following help ...
geo metadata written 6 months ago by EverInEarnest30 • updated 6 months ago by Sean Davis24k
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Comment: C: Converting between drug identifier formats
... Thanks, Wolf! That resource looks very useful; I will check it out. ...
written 7 months ago by EverInEarnest30
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Comment: C: Converting between drug identifier formats
... Many thanks, Zhilong! That is exactly what I needed! ...
written 7 months ago by EverInEarnest30
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Converting between drug identifier formats
... I have two CSV files of drug-related data. One has the drug info specified with CHEMBL identifiers, whereas the second file contains DrugBank and PubChem IDs. I need to compare these two files for overlap in their drug contents. Both files contain drug names in string format, but working with those ...
database drug conversion written 7 months ago by EverInEarnest30 • updated 7 months ago by Wolf Ihlenfeldt40
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Comment: C: Formatting problem when converting from UniProt to Entrez Gene ID format
... Many thanks for your detailed response, Kevin; I have also been exploring another route, and will consider your suggestions along with my current efforts; I'll plan to post what works. ...
written 9 months ago by EverInEarnest30
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Comment: C: How to obtain DrugBank Drug Name and SMILES Data from DrugBank ID?
... Thank you, cannin!! I will try your strategy. ...
written 9 months ago by EverInEarnest30
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Formatting problem when converting from UniProt to Entrez Gene ID format
... My code below reads in a file of a subset of the DrugBank data, and then calls UniProt.ws() to map the UniProt IDs of the drug targets to Entrez Gene ID format. This code runs and generates the output file, but the output is incorrect, and I am confused by the following issues: My input file contai ...
R uniprot conversion entrez written 9 months ago by EverInEarnest30 • updated 9 months ago by Kevin Blighe21k
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Comment: C: How to obtain DrugBank Drug Name and SMILES Data from DrugBank ID?
... Could you clarify where the SMILES file and other similar DrugBank files are available? I have reviewed the DrugBank site's contents, and see the full database available for download, as well as this page: https://www.drugbank.ca/releases/latest#protein-identifiers that allows download of the target ...
written 9 months ago by EverInEarnest30
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Comment: C: How to obtain DrugBank Drug Name and SMILES Data from DrugBank ID?
... Thanks for your suggestion, Bjorn; I will pursue your suggested method. ...
written 9 months ago by EverInEarnest30

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