Open agitter opened 5 years ago
GENIE3 is a popular network inference approach. It provides a way to output all regulator-target edges: https://github.com/aertslab/GENIE3/blob/master/vignettes/GENIE3.Rmd#L116
SINGE already has a similar output format but does not output edges with a score of 0. The 0s in the output are edges that had a non-zero score before rounding https://github.com/gitter-lab/SINGE/blob/8e75a502885552165cd40f1e53a6feeb4ee8b9c2/code/SCINGE.m#L38
We could consider adding an optional parameter in the config file that would output all edge scores and all regulator scores even if they are 0. That would help users use SINGE in downstream analyses set up for GENIE3.
GENIE3 is a popular network inference approach. It provides a way to output all regulator-target edges: https://github.com/aertslab/GENIE3/blob/master/vignettes/GENIE3.Rmd#L116
SINGE already has a similar output format but does not output edges with a score of 0. The 0s in the output are edges that had a non-zero score before rounding https://github.com/gitter-lab/SINGE/blob/8e75a502885552165cd40f1e53a6feeb4ee8b9c2/code/SCINGE.m#L38
We could consider adding an optional parameter in the config file that would output all edge scores and all regulator scores even if they are 0. That would help users use SINGE in downstream analyses set up for GENIE3.