A tool for inferring gene regulatory networks by expression data.
mvn install -DskipTestsjava -Xmx8G -jar target/grn_inferer.jar -w 100000 -s 1 -r 20 -g ge.tsv -o out -m 1Expression data is provided as a single tab separated file. Columns correspond to genes while rows represent different unnamed experiments. An example of ge.tsv file:
| APOE | CTF1 | EGR1 | MAPK8 | POLB |
|---|---|---|---|---|
| 0.816 | 0.258 | 0.442 | 0.178 | 0.646 |
| 0.558 | 0.714 | 0.347 | 0.802 | 0.852 |
| 0.440 | 0.572 | 0.813 | 0.729 | 0.844 |
| 0.022 | 0.833 | 0.580 | 0.690 | 0.780 |
| 0.860 | 0.864 | 0.901 | 0.867 | 0.545 |
Currently, sipmle discretization is applied to values, so the absolute values are not taken into account, only order of values for each gene is important.
See help for more information.
java -jar target/grn_inferer.jar -h