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Murali-group / Beeline

BEELINE: evaluation of algorithms for gene regulatory network inference
GNU General Public License v3.0
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adding new files #55

Closed xPandasx closed 3 years ago

xPandasx commented 3 years ago

Hi, I recently downloaded Beeline for my Bachelor thesis and Beeline comes along with example Datasets already which i could calculate. I wanted to use my own Datasets or from the https://zenodo.org/record/3701939 website. I wanted to make sure which zip, from the two listed there, i should download and where to implement them or in which files i need to change the exaple datasets with the new ones Thanks for your help

ktakers commented 3 years ago

Thank you for using BEELINE. Please download and extract the BEELINE-data.zip file under the root directory for BEELINE, which should populate the input and config-files directories with data and configuration for synthetic, curated, and scRNA-seq benchmarks. The YAML files under config-files can be used instead of config-files/config.yaml to run the benchmarks for each dataset, for example:

python BLRunner.py --config config-files/Curated/GSD.yaml

Please refer to the README.txt in BEELINE-data.zip regarding the directory structure and the expected content for each file if you would like to add your own datasets.

The BEELINE-Networks.zip file contains the reference networks for the evaluation of the scRNA-seq datasets, and can be extracted following that directory structure under input.