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zhangdb authored May 21, 2022
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# SIGNET User's Manual

## Copyright of SIGNET

The core of current version of SIGNET is to use the two-stage least squares approach proposed by [Chen et al. (2018)](https://www.jmlr.org/papers/volume19/16-225/16-225.pdf) to construct genome-wide gene regulatory networks.

## System Requirement

SIGNET runs on a **UNIX bash shell**. Check your shell with `echo $SHELL` to make sure that you are running on UNIX bash shell. SIGNET uses the **Slurm Workload Manager** for high performance computing (HPC) clusters in its stage of constructing the gene regulatory network in parallel. **Zhongli: How to check whether the system uses SLURM?**
Expand All @@ -25,11 +29,9 @@ There are two ways to install the required packages for SIGNET: (1) Install Sing

While you can install all of these packages in your sever, we would rather suggest you to install Singularity and use the Singularity container `signet.sif` coming with SIGNET. Here is a list of packages SIGNET runs on:

- PLINK
- PLINK
- IMPUTE2
- ...


- R & its libararies.



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