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PharmacoGx:::.summarizeSensitivityNumbers, or equivalently the table returned by sensNumbers is sometimes a slight misrepresentation of the actual data available in Profiles, due to various QC filters…
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PharmacoGx version 2.4.0
## CCLE vs GDSC1 (similar to Haibe-Kains Nature 2013)
ccle
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We have been granted access to the UK Biobank.
We should explore their online platform: https://www.ukbiobank.ac.uk/enable-your-research/research-analysis-platform
There are at least two article…
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Yes, its not very informative, but it is a required column for pharmacogx to work.
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I just noticed this right now while trying to respond to a user issue for `PharmacoGx`.
When we migrated the `availablePSets` and `downloadPSet` functions to query the ORCESTRA API we started forci…
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Hello ORCESTRA team,
I am moving [this ](https://github.com/bhklab/PharmacoGx/issues/80) issue here from PharmacoGx since we source all PSets from ORCESTRA now:
@bhaibeka
> "Gender" in cellInf…
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Here is the code and error massage:
```
library(PharmacoGx)
load("PSets/CTRPv2.RData")
ctcells
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https://github.com/bhklab/PharmacoGx/blob/eeee68a021549bdfab23e85cdf57c15ae54a52cc/R/methods-summarizeMolecularProfiles.R#L227
Im about 60% sure this is supposed to be a 2 in the if statement, it d…
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Hi,
I am wondering, are the transcripts expression values in the `CCLE_hs.RData` file quantified in log2(FPKM+1)?
There are values that seem more like count ...
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It appears that the cell line metadata for GDSC1000 (and likely other datasets, assuming they were processed in a similar manner) is corrupted some cell lines.
Specifically, cell lines which contai…