List of networks per replicate with edge weights re-scaled between 0 and 1, and gene pairs (edges) with overlapping annotations removed. The networks were inferred using GRNBoost2 based on a subset of the primate neural differentiation scRNA-seq dataset. All 300 genes in the subsetted data were used as potential regulators. To circumvent the stochastic nature of the algorithm, GRNBoost2 was run 10 times on the same count matrices, then the results were averaged across runs, and rarely occurring edges were removed altogether. In addition, edges inferred between the same gene pair but in opposite directions were also averaged. Edge weights were scaled by the maximum edge weight across all replicates. Gene pairs that have overlapping annotations in any of the species' genomes were removed from all networks.
Format
A named list of 9 [igraph] objects. Each network contains 300 nodes, and has 1 node attribute and 3 edge attributes:
Node attributes:
- name
Name of the node (gene).
Edge attributes:
- weight
Edge weight, the importance score calculate by GRNBoost2 rescaled between 0 and 1.
- genomic_dist
Numeric, the genomic distance of the 2 genes that form the edge (Inf if the 2 genes are annotated on different chromosomes/contigs).