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bhklab/PharmacoGx
Problem with availablePSets() and downloadPSet()

Hi, When I used the availablePSets() command, it returns me the following error: Error in parse_con(txt, bigint_as_char) : lexical error: invalid char in json text. Please use the correct dataset (right ...
  • CCCC1800
  • Opened 
    4 days ago
  • #168

bhklab/PharmacoGx
Unable to retrieve datasets

unable to pull datasets or view which are available gdsc - downloadPSet( CMAP_2016 ) Error in parse_con(txt, bigint_as_char) : lexical error: invalid char in json text. Please use the correct dataset ...
  • tischfis
  • 2
  • Opened 
    on Feb 19
  • #167

bhklab/PharmacoGx
Can't access the data

I can not access the data from: https://www.pmgenomics.ca/bhklab/sites/default/files/downloads/ # library(CoreGx) library(PharmacoGx) # Both commands do not work availablePSets() downloadPertSig( CMAP ...
  • mildamarij
  • 2
  • Opened 
    on Dec 16, 2024
  • #166

bhklab/PharmacoGx
bug: validation of new pset creation displays wrong error

hasValidSamples - sampleIdL %in% samples if (!all(all(hasValidSamples))) { nmsg - .formatMessage( All sampleids in the @molecularProfiles slot\n must also be in the @sample ...
  • jjjermiah
  • Opened 
    on Dec 11, 2024
  • #165

bhklab/PharmacoGx
Re-processing CTRPv2 raw sensitivity data

Hi team, I have been looking at the CTRPv2 sensitivity data here to re-process it myself; however, none of the measurements are actually raw intensity values. For example, their so called raw data has ...
  • MomenehForoutan
  • Opened 
    on Oct 25, 2024
  • #164

bhklab/PharmacoGx
SMILES in PSets

Hi team, I have been checking the SMILES for several drugs from PRISM PSet manually and they do not seem to be consistent with those from PubChem. I also tried retrieving SMILES using the webchem package ...
  • MomenehForoutan
  • Opened 
    on Sep 12, 2024
  • #163

bhklab/PharmacoGx
Update of Datasets to Recent Versions?

Hi!! Will there be an update to include more recent versions of the datasets?
  • KatynaSada
  • Opened 
    on Jul 9, 2024
  • #162

bhklab/PharmacoGx
Issue with drugPerturbationSig function in PharmacoGx package

I am writing to bring to your attention an issue I encountered while using the drugPerturbationSig function in the PharmacoGx package. I recently attempted to use the function with the following code: ...
  • pijush1285
  • Opened 
    on Apr 29, 2024
  • #161

bhklab/PharmacoGx
Static QC Updates for new GDSC Pset

Static QC checks: 1. summarizeSensitivityProfiles() Error: [CoreGx::assay] There is no assay profiles in this LongTable. Use assayNames(longTable) for a listof valid assay names. 2. assay() returns ...
  • raymond126
  • 2
  • Opened 
    on Apr 12, 2024
  • #160

bhklab/PharmacoGx
Add better GHA to packages

insightsengineering organization has some great workflows and a great template. https://github.com/insightsengineering/r.pkg.template/actions/runs/8377084358/workflow - [ ] Add the Version bump - ...
enhancement
  • jjjermiah
  • Opened 
    on Apr 8, 2024
  • #157
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