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archive_script
archive_script
 
 
manuscript
manuscript
 
 
postGWAS_pipeline
postGWAS_pipeline
 
 
regenie_pipeline
regenie_pipeline
 
 
saige_pipeline
saige_pipeline
 
 
util
util
 
 
.lintr
.lintr
 
 
README.md
README.md
 
 
get_path_icd10_refined.r
get_path_icd10_refined.r
 
 
get_pathogen_taxonomy.R
get_pathogen_taxonomy.R
 
 
gwas_phenotypes.r
gwas_phenotypes.r
 
 
gwas_stratify.r
gwas_stratify.r
 
 
gwas_summary.ipynb
gwas_summary.ipynb
 
 
gwas_summary.py
gwas_summary.py
 
 
hes_filter_summary.tsv
hes_filter_summary.tsv
 
 
hes_what_to_analyse.r
hes_what_to_analyse.r
 
 
map_bugbank_ukbEID.r
map_bugbank_ukbEID.r
 
 
qc_summary.ipynb
qc_summary.ipynb
 
 
qc_summary.r
qc_summary.r
 
 
replot_manhattan.sh
replot_manhattan.sh
 
 
requirements.yml
requirements.yml
 
 
sanity_check.ipynb
sanity_check.ipynb
 
 
setup.sh
setup.sh
 
 
sgss_filter_summary.tsv
sgss_filter_summary.tsv
 
 
sgss_what_to_analyse.r
sgss_what_to_analyse.r
 
 
ukb_filter_summary.tsv
ukb_filter_summary.tsv
 
 
worklog.md
worklog.md
 
 

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Bugbank analysis

This respository for analysing the Bugbank.

Bugbank is a project that link the infection database from UK Health Security Agency with the human database UK Biobank (UKB). This linkage is meant to provide an enhancment for infection data in UKB and thereby improve research of infection diseases.

Here we try to conduct a baseline analysis on the potential of Bugbank linkage to improve the identification of human genetic risk factors for common pathogens in England

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