New features

Added support for Solanum lycopersicum (tomato) (see folder data_sly).
Added support to omit the motif enrichment analysis. In this mode, all possible species are supported, but note that the resulting networks are more prone to false positives.
Added a new output format: edge table with regulon rank and edge weights.
Added regulator heatmap as additional output figure (example).
Enrichment background is now filtered for expressed genes, usually leading to an increased number of predicted regulons.
When computing enrichment: minimum number of hits is set to 2 to relax FDR statistics.
Updated gene GO annotation for Arabidopsis.
Added gene alias file for Zea mays.
Added input file validation step.
Dataset statistics are printed after the input validation step.

Documentation

Added the pipeline schema with detailed explanations to the README.
Added constraints for the input files in Prepare your files.
Added an example of the expression matrix generation from a Seurat object in Prepare your files.
Added the FAQ.

Full Changelog: v1.0...v2.0