The code in this package is intended to specifically run the analysis as it appears in Eng, Aeschlimann, van Veenendaal et al., PLOS Medicine 2019. We will be releasing a generalized version of our multilayer non-negative matrix factorization (NMF) workflow with a subsequent paper.
For data access, please contact Dr. Susanne Benseler, chair of the Canadian Association of Paediatric Rheumatology (CAPRI), who will forward your request to the CAPRI Scientific Protocol Evaluation Committee/Data Access Committee.
This analysis requires Python 3.6 or higher.
We recommend managing your Python installation using conda,
especially as we provide an environment.yml file for your convenience.
Please install R 3.5.0+ with the following packages:
carggbeeswarmlmtestmoments
To generate the wheel figure, Circos 0.69+ is needed. The most straightforward way to do
so is to install coreutils through Homebrew and then issuing the
command
brew install circos
On macOS, coretools must be installed (due to the gln command, required for properly
linking inputs and outputs). The most straightforward way to do so is to install
coreutils through Homebrew and then issuing the command
brew install coreutils
To preview what rules will be run, type
snakemake --dry-run everything
To run the analysis, type
snakemake everything
If you wish to run the analysis on a cluster, type
snakemake --cmd '<command>' everything
where <command> is the command you would use to submit a job (e.g., qsub).
To clean all output files, type
snakemake --delete-all-output