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GenePrioritization.md

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GenePrioritization tool help

GenePrioritization (2024_08-113-g94a3b440)

Performs gene prioritization based on list of known disease genes of a disease and a PPI graph.

Mandatory parameters:
  -in <file>        Input TSV file with one gene identifier per line (known disease genes of a disease).
  -graph <file>     Graph TSV file with two gene identifiers per line (PPI graph).
  -out <file>       Output TSV file containing prioritized genes for the disease.

Optional parameters:
  -method <enum>    Gene prioritization method to use.
                    Default value: 'flooding'
                    Valid: 'flooding,random_walk'
  -n <int>          Number of network diffusion iterations (flooding).
                    Default value: '2'
  -restart <float>  Restart probability (random_walk).
                    Default value: '0.4'
  -debug <file>     Output TSV file for debugging
                    Default value: ''

Special parameters:
  --help            Shows this help and exits.
  --version         Prints version and exits.
  --changelog       Prints changeloge and exits.
  --tdx             Writes a Tool Definition Xml file. The file name is the application name with the suffix '.tdx'.
  --settings [file] Settings override file (no other settings files are used).

GenePrioritization changelog

GenePrioritization 2024_08-113-g94a3b440

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