ChristopherEeles
commented
1 year ago - Add basic template for drug combo vignette
- Fitting monotherapy curves for Mathews Griner dataset vignette
- Preparing to compute synergy metrics in Mathews Griner vignette
- Computed synergy Null references for Mathews Griner vignette
- Fix bug in estimateProjParams caused by dropping zero concentration in .reformatData
- Fix bug is estimateProjParams caused by passing lower_bounds as upper_bounds in .fitCurve2 call
- Fix bug in estimteProjParams where E)inf was being unlogged instead of EC50
- Fix names of returned arguments in estimateProjParams such that EC50 and E_inf are assigned to the correct columns
- Add ZIP delta calculation to vignette, but results seem wrong; need to audit the code
- Update remote
- Adding plots to determine appropriate Rsquared filter to get better agreement between synergy metrics
- Clustering monotherapy curves to look for bad fit trends * Also cleaned up some code formatting in filterNoisyCurves.R
- Clustering by actual or predicted viability partitions curves into broader response patterns
- Add bibliography for drug combinations vignette
- Add description of Mathews Griner dataset to drug combos vignette
- Fix missing values and cleaned up drug synergy visualization
- Finished TRE creation section of vignette
- Completing monotherapy curve fit section of drug combo vignette
- Finalizing text for drug combination vignette
- Finished all vignette text, knitting to proof read
- Finished first pass proof read
- Finalized edits for drug synergy vignette