pfeiljx/taux repository overview

docker run pfeiljx/taux -h
taux -x expression-data.tsv -l label-data.tsv:
  -h [ --help ]                         Display this help message
  -x [ --expression ] arg               Path to expression matrix in TSV format
  -l [ --label ] arg                    Path to sample labels in TSV format
  -r [ --strata ] arg                   Path to strata for cross validation
                                        sampling
  --mode arg                            Runs analysis in sensitive mode
  -n [ --normalize ]                    MinMax normalize expression data
  -t [ --threshold ] arg (=3)           T-statistic threshold for filtering
                                        ratios
  -p [ --splits ] arg (=1)              Number of parallel splits to use.
  -c [ --cpus ] arg (=16)               Number of parallel splits to use.
  -u [ --mean-filter ] arg (=1)         mean expression filter. Default (1.0)
  -v [ --var-filter ] arg (=80)         Expression variance filter. Take top %
                                        of most variable genes. Default (80)
  -m [ --min-subtype ] arg (=5)         Absolute number of samples to be
                                        considered a subtype.
  -o [ --output ] arg (=taux-output.tsv)
                                        Path to output file
  -d [ --debug ]                        Debug mode.