Improved gene prioritization in crops using single-cell gene regulatory networks and text mining

This repository contains the input and output data associated with the analyses presented in the article "Improved gene prioritization in crops using single-cell gene regulatory networks and text mining". Provided files: MINI-EX__input.zip: Contains one directory per scRNA-seq dataset used in the study. Each directory includes the input files derived from the respective scRNA-seq data. MINI-EX__output.zip: Contains one directory per analysis performed in the study. Each directory includes the output files generated by MINI-EX and, when applicable, the functional prior used in the run. Output folder naming conventions: For Arabidopsis thaliana runs: folder names follow the format ref__ms-XX__oc-YY, where: ref: indicates that the run was performed using the "reference" procedure ms-XX: specifies the maximum triple score threshold used (e.g., XX = 80) oc-YY specifies the minimum number of triple occurrences used (e.g., YY=30) For Zea mays runs: folder names follow the format ref__zma__ms-XX__oc-YY__ortho-1-to-N__ms-AA__oc-BB, where: ref indicates that the "reference" procedure was used zma indicates that species-specific triples for Z. mays were used, with the applied filters specified by ms and oc ortho-1-to-N indicates that triples transferred via orthology were included (where N is 1, 2 or 3), with their respective filters specified by ms and oc