Effect of vanzacaftor on cystic fibrosis airway epithelial cells compared to elexacaftor - Data and statistical analysis

Data and code to reproduce all statistical analyses and figures in the manuscript. Compiled outputs from the reports are available in files "organoids.docx" and "nc.docx".

The `code.zip` archive contains the source code. The file "organoids.qmd" reproduces the organoid analyses, file "nc.qmd" reproduces the analysis for human nasal epithelial cells. Other files are supporting to let the main analysis run.

The analysis is written in R + Quarto.

The renv package is used for recreate the computational environment.

The patient-derived organoids dataset is stored in the file `organoids_data.csv`, the columns are:

• `well` The ID of the well within the plate the measurement was taken
• `time` time from start of measurement
• `area` area of the organoids
• `patient` Anonymized ID of the patient
• `date` Date when the experiment was performed (date and patient ID identify the plate)
• `filename` The filename in raw data (not published) this plate was stored in.  (uniquely identifies a plate)
• `mix` Identifies one od two variants of plate layouts used
• `replicate` ID of technical replicate (two technical replicates were done for each condition on the same plate)
• `type` The main condition - one of "VTI" (Vanzacator + Tezacaftor+Ivacaftor), "VTI_2", "VTI_02", "VTI_002" (same as VTI, but differing concentrations of Vanzacaftor - 2, 0.2 and 0.02 μM) "ETI" (Elaxacaftor + Tezacaftor+Ivacaftor", "FskOnly" (Control, only forskolin)
• `fsk_concentration` concentration of forskolin (μM)

The human nasal epithelial cells dataset is stored in the file `nc_data.csv` the columns are:

• `id` anonymized ID of the patient
• `pretreatment` how the cells were treated - values: "Untreated", "ETI" (Elaxacaftor + Tezacaftor+Ivacaftor", "VTI" (Vanzacator + Tezacaftor+Ivacaftor), "Healthy_Ind0" - "Healthy_Ind50" (cells from healthy donors, treated with varying concentrations of indomethacin)
• `rt_start` resistance at start of experiment (Ω*cm2)
• `basal`,`ami`,`fsk_max_peak`,`fsk_final`,`vx770`,`inh172`,`atp` Isc values at individual time points (μA/cm2)
• `repl_id` unique ID for each row