Supported Algorithms

The following table lists the algorithms and the parameters they accept, along with default parameter values.

Algorithm

Input Parameters

SINCERITIES

  • nBins : (Default = 10)

SCODE

  • z : (Default = 10)

  • nIter : (Default = 1000)

  • nRep : (Default = 6)

SINGE

  • lambda : (Default = 0.01)

  • dT : (Default = 15)

  • num_lags : (Default = 5)

  • kernel_width : (Default = 0.5)

  • prob_zero_removal : (Default = 0)

  • prob_remove_samples : (Default = 0.0)

  • family : (Default = ‘gaussian’)

  • num_replicates : (Default = 6)

PPCOR

  • pVal : p-value cutoff (Default = 0.01)

PIDC

None

PEARSON

None

LEAP

  • maxLag : (Default = 0.33)

JUMP3

None

SCRIBE

  • delay : (Default = 5)

  • method : Any of ‘RDI’, ‘uRDI’, ‘cRDI’, or ‘ucRDI’ (Default = ‘ucRDI’)

  • lowerDetectionLimit : (Default = 0)

  • expressionFamily : If mRNA counts, use ‘negbinomial’ (Default = ‘uninormal’)

  • log : Log transform expression values (Default = False)

  • ignorePT : Ignore pseudotime (Default = True)

SCSGL

  • pos_density : Density of positive edges in the inferred network

  • neg_density : Density of negative edges in the inferred network

  • assoc : Association measure used for graph learning

GRNVBEM

None

GRISLI

  • L : (Default = 10)

  • R : (Default = 3000)

  • alphaMin : (Default = 0.0)

GENIE3

None

GRNBOOST2

None