Multi-omics data harmonisation for the discovery of COVID-19 drug targets

• Update documentation to specify dependencies more clearly
• Enable zenodo synchronisation

v1.2.3 contains major pipeline updates, including to the API, the way optimal hyperparameters are stored and handled, and parallelisation. Also removed redundant plots and correctly skipped cases where the number of components are too few for a 2D plot. Replaced the existing case study with a separate, simplified case study, which is compatible with our latest pipeline API. Reworked installation to fix dependency issues, and included new automated tests. Repository now contains information about R version compatibility and operating system requirements. Main repository moved to github (but is still available on gitlab).

• We present a generic, flexible, reproducible, open-access data harmonisation framework that can be scaled out to future multi-omics analysis to study a phenotype in a holistic manner.
• Our git repository along with code, documentation and sample data on three case studies are available with install instructions.
• Docker and singularity images are available only for the initial version of the software used to generate the results in the Briefings in Bioinformatics manuscript.
• The pipeline can be installed as an R package with the following commands:

# tested on R 4.2.3 for linux
install.packages("devtools")
devtools::install_git("https://github.com/tyronechen/SARS-CoV-2.git", subdir="multiomics", build_vignettes=FALSE, INSTALL_opts="--no-multiarch")

# or through the command line
Rscript -e 'install.packages("devtools"); devtools::install_git("https://github.com/tyronechen/SARS-CoV-2.git", subdir="multiomics", build_vignettes=FALSE, INSTALL_opts="--no-multiarch")'