Analysis done for the BrepPhylo paper on COVID, Ebola and RSV repertoires
Joseph Ng (@josef0731), July 2021
This repository contain R markdown notebooks for analysis performed for this work. Both the R markdown files and the HTML notebooks are available.
ClonalDiversity: Analysis of clonal diversity (clone size, gini diversity etc) (HTML notebook)convergence-ebola: Analysis for 'convergent' sequences from the repertoire shared across Ebola patients, and converging towards known binders of Ebola virus proteins from the literature. (HTML notebook)convergence-covid: Analysis for 'convergent' sequences from the repertoire shared across COVID-19 patients, and converging towards known binders of SARS-CoV-2 proteins from the literature. (HTML notebook)convergence-RSV: Analysis for 'convergent' sequences from the repertoire shared across volunteers (infected/uninfected) in the RSV live challenge trial, and converging towards known binders of RSV proteins from the literature. (HTML notebook)convergence-all: Analysis for 'convergent' sequences from the repertoire shared across RSV, Ebola and COVID-19 repertoires and healthy controls incoporating known binders of Ebola/SARS-CoV-2/RSV proteins in the literature.(HTML notebook)CSR: Analysis of frequency and distance-from-germline of Class-Switch Recombination events detected from lineage trees. (HTML notebook)GeneUsage: Analysis of V, D, J gene usage. Separation by age groups. (HTML notebook)MutationalLevels: Analysis of mutational levels in lineage trees. (HTML notebook)Subsampling: Analysis of the effect of sequencing depths on the robustness of the statistics deployed in the analysis, by random subsampling of sequences. (HTML notebook)
Note: These rendered HTML notebooks depend on an online renderer to display the notebooks. As such, the network visualisation for the convergent network clusters (in the convergence-* noteboks) does not work. Please download the HTML files and open them locally in an browser to properly visualise these networks.
known_binders: Curation of known antibodies targetting specific antigens from the Protein Data Bank (PDB) & from the literature.
convergent_overlap.bib: references used in the convergent network analysis in bibtex format.