Direct Inference evidence-based predictions
Automated pipeline
We provide an automated pipeline using pyrpipe and snakemake. This pipeline can be easily configured and executed in an automated manner (HIGHLY RECOMMENDED).
The automated pipeline can be easily scaled on an HPC by executing multiple samples in parallel. We recommend using this implementation of the pipeline for simplicity of use and reproducibility of results.
The pipeline can easily be modified and shared. For additional information see: pyrpipe (https://doi.org/10.1093/nargab/lqab049) and orfipy (https://doi.org/10.1093/bioinformatics/btab090) pipelines.
Direct Inference prediction by steps
If you prefer to run the Direct Inference pipeline step by step, the details are explained below.