Code for systems analysis of KSPZV1 malaria vaccine trial.
Unsupervised clustering heatmaps Figures 1B and S2, Complex heatmap and downstream clustering analyses, pre-immunization baseline (REVISED)
Figures 4A and S5, Complex heatmap and downstream clustering analyses, delta (REVISED)
Differential gene expression and enrichment analysis Figures 2D, S3B, DGE and GSEA between protected and not protected by treatment group, pre-immunization baseline (REVISED)
Figure 2E, IPA Upstream Regulator between protected and not protected by treatment group, pre-immunization baseline (REVISED)
Figures 3A-C, CSP IgG and flow cytometry features that correlate with time-to-first-parasitemia (6 months) followed by GSEA
Figures 3D and 3E, DGE and GSEA between CSP-specific IgG high responders vs low responders in 1.8x10^6 PfSPZ treatment group, pre-immunization transcriptomes
Figures 4D, 4E, 4F, Tables S3, S4, DGE and GSEA within and between Δ protected and Δ not protected for 1.8x10^6 PfSPZ group (REVISED)
Figures S4A, S4B, S4C, pre-immunization baseline DGE and GSEA comparison for KSPZV1, VRC 312, VRC 314, and BSPZV1 studies
Weighted gene correlation network analyses Figures 2A, 2B, 2C. WGCNA, pre-immunization baseline (REVISED)
Figures 4B, 4C, S6A, S6B, WGCNA, Δ (post-vax/baseline) (REVSED)
Machine learning (class prediction) Figures 6B, S7A, XGBoost, 1.8x10^6 PfSPZ, pre-immunization baseline (REVISED)
ML code to run XGBoost models using 1.8x10^6 PfSPZ, pre-immunization baseline features (REVISED)
Figures 6C, S7B, XGBoost, 1.8x10^6 PfSPZ, post-vaccination (REVISED)
ML code to run XGBoost models using 1.8x10^6 PfSPZ, post-vaccination features (REVISED)
Figures 6D, S7C, XGBoost, 1.8x10^6 PfSPZ, delta (REVISED)
ML code to run XGBoost models using 1.8x10^6 PfSPZ, delta features (REVISED)
Figures 6E, S7D, XGBoost, Placebo, pre-immunization baseline (REVISED)
ML code to run XGBoost models using Placebo, pre-immunization baseline features (REVISED)
Integrated, multi-modal correlations and network plots Figure 5, Spearman correlations between BTMs, flow cytometry features, cytokines (baseline only) and CSP-specific IgG response and time-to-first parasitemia through 6 month surveillance
Spearman correlations between gene expression, flow cytometry features, cytokines (baseline only) and CSP-specific IgG response and time-to-first parasitemia through 6 month surveillance
FSTL4 heatmap from other datasets (NEW)
=======