EvitaH/QECHospitalKlebs

Data and code repository for a study to understand longitudinal population genomics of Klebsiella pneumoniae in Queen Elizabeth Central Hospital, Blantyre, Malawi # QECHospitalKlebs The QECHKlebs R package is a repository for data generated and reproducible analysis scripts for the manuscripts arising from this study: **Longitudinal analysis within one hospital in sub-Saharan Africa over 20 years reveals repeated replacements of dominant clones of Klebsiella pneumoniae and stresses the importance to include temporal patterns for vaccine design considerations** Eva Heinz 1,2 , Oliver Pearse 2,3 , Allan Zuza 3 , Sithembile Bilima 3 , Chisomo Msefula 4 , Patrick Musicha 2,3 , Patriciah Siyabu 5 , Edith Tewesa 5 , Fabrice E Graf 2 , Rebecca Lester 3,6 , Samantha Lissauer 3,7 , Jennifer Cornick 3,7 , Joseph M Lewis 2,3,7 , Kondwani Kawaza 3,4 , Nicholas R Thomson 8,9 , Nicholas A Feasey 2,3,10 1. Department of Vector Biology, Liverpool School of Tropical Medicine, Liverpool, UK 2. Department of Clinical Sciences, Liverpool School of Tropical Medicine, Liverpool, UK 3. Malawi Liverpool Wellcome Programme, Kamuzu University of Health Sciences, Blantyre, Malawi 4. Kamuzu University of Health Sciences, Blantyre, Malawi 5. Queen Elizabeth Central Hospital, Blantyre, Malawi 6. Division of Infection & Immunity, University College London, UK 7. Department of Clinical Infection, Microbiology and Immunology, University of Liverpool, Liverpool, UK 8. Parasites and Microbes Program, Wellcome Sanger Institute, Hinxton, UK 9. London School of Hygiene and Tropical Medicine, London, UK 10. School of Medicine, St Andrews University, UK Paper currently available as pre-print here ## Installation If you just want the data, then all the data to replicate the analysis are bundled with the package. To install the package from GitHub: ``` r install.packages("devtools") devtools::install_github("github.com") ``` The various data objects are described in the pkgdown site for this package here, and available via R in the usual way. They are all lazy loaded so will be available for use immediately. ### …