Afrah-Khairallah/somascan-host-proteins-sarscov2

Domain:

healthcare

Creator:

Afr

Host:

Code and workflows for the study “Host proteins associated with strong neutralizing SARS-CoV-2 antibody responses in a South African cohort.” Includes R scripts for SomaScan® proteomics analysis, identifying host proteins, pathways, and predictors linked to neutralizing antibody responses somascan-host-proteins-sarscov2 Code and workflows for the study “Host proteins associated with strong neutralizing SARS-CoV-2 antibody responses in a South African cohort.” Includes R scripts for SomaScan® proteomics analysis, identifying host proteins, pathways, and predictors linked to neutralizing antibody responses. --- \## Data files used for each figure \### Figure 2 \*\*Figure 2A – data used is here:\*\* \- `data/cleaned/cleanedData\_150625.csv` \*\*Figure 2B \& 2C – data used is here:\*\* \- `data/cleaned/Merged\_Metadata\_with\_Outpatient\_Days.csv` \- `data/cleaned/min\_max\_tooutpatient.csv` \*\*Figure 2D – data used is here:\*\* \- `data/cleaned/Merged\_Metadata\_with\_Outpatient\_Days.csv` \- `data/cleaned/min\_max\_tooutpatient.csv` \*\*Figure 2E \& 2F – data used is here:\*\* \- `data/cleaned/Merged\_Metadata\_with\_Outpatient\_Days.csv` \- `data/cleaned/min\_max\_tooutpatient.csv` --- \### Figure 3 \*\*Figure 3A – data used is here:\*\* \- `data/proteins/allProteins/D614GNeutralization/fullResultsD614GNeutralization\_170625.csv` \- `data/proteins/threshProteins/D614GNeutralization/threshResultsD614GNeutralizationFDR\_0.05\_170625.csv` \*\*Figure 3B \& 3C – data used is here (full results):\*\* \- `data/allProteins/SuppO2\_Binom/fullResultsSuppO2\_Binom\_170625.csv` \- `data/allProteins/Neuts\_Binom/fullResultsNeuts\_Binom\_170625.csv` \- `data/allProteins/Spike.D614G\_tp2\_Binom/fullResultsSpike.D614G\_tp2\_Binom\_170625.csv` \*\*Figure 3B \& 4C – data used is here (thresholded, FDR < 0.05):\*\* \- `data/proteins/threshProteins/SuppO2\_Binom/threshResultsSuppO2\_Binom\_FDR0.05\_170625.csv` \- `data/proteins/threshProteins/Neuts\_Binom/threshResultsNeuts\_Binom\_FDR0.05\_170625.csv` \- `data/proteins/threshProteins/Spike.D614G\_tp2\_Binom/threshResultsSpike\_D614G\_tp2\_Binom\_FDR0.05\_170625.csv` \- `data/proteins/threshProteins/D614GNeutralization/threshResultsD614GNeutralizationFDR\_0.05\_170625.c …

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