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**Note about Seurat v5:** We plan to test the compatibility of hdWGCNA with[Seurat version 5](https://satijalab.org/seurat/articles/get_started_v5.html). with Seurat v5, but we have currently not updated hdWGCNA to work with Seurat v5. We strongly suggest using Seurat v4 at this time, or use v5 at your own risk.

**Note about Seurat v5:** We plan to test the compatibility of hdWGCNA with [Seurat version 5](https://satijalab.org/seurat/articles/get_started_v5.html), but we have currently not updated hdWGCNA to work with Seurat v5. We strongly suggest using Seurat v4 at this time, or use v5 at your own risk.

If you use hdWGCNA in your research, please cite the following papers in addition to the original WGCNA publication:

<p>hdWGCNA is an R package for performing weighted gene co-expression network analysis <a href="https://horvath.genetics.ucla.edu/html/CoexpressionNetwork/Rpackages/WGCNA/" class="external-link">(WGCNA)</a> in high dimensional transcriptomics data such as single-cell RNA-seq or spatial transcriptomics. hdWGCNA is highly modular and can construct co-expression networks across multi-scale cellular and spatial hierarchies. hdWGNCA identifies robust modules of inerconnected genes, and provides context for these modules through various biological knowledge sources. hdWGCNA requires data formatted as <a href="https://satijalab.org/seurat/index.html" class="external-link">Seurat</a> objects, one of the most ubiquitous formats for single-cell data. Check out the <a href="https://smorabit.github.io/hdWGCNA/articles/basic_tutorial.html">hdWGCNA in single-cell data tutorial</a> or the <a href="https://smorabit.github.io/hdWGCNA/articles/ST_basics.html">hdWGCNA in spatial transcriptomics data tutorial</a> to get started.</p>

<p><strong>Note about package development:</strong> hdWGCNA is under active development, so you may run into errors and small typos. We welcome users to write <a href="https://docs.github.com/en/issues/tracking-your-work-with-issues/creating-an-issue" class="external-link">GitHub issues</a> to report bugs, ask for help, and to request potential enhancements.</p>

<p><strong>Note about Seurat v5:</strong> We plan to test the compatibility of hdWGCNA with<a href="https://satijalab.org/seurat/articles/get_started_v5.html" class="external-link">Seurat version 5</a>. with Seurat v5, but we have currently not updated hdWGCNA to work with Seurat v5. We strongly suggest using Seurat v4 at this time, or use v5 at your own risk.</p>

<p><strong>Note about Seurat v5:</strong> We plan to test the compatibility of hdWGCNA with <a href="https://satijalab.org/seurat/articles/get_started_v5.html" class="external-link">Seurat version 5</a>, but we have currently not updated hdWGCNA to work with Seurat v5. We strongly suggest using Seurat v4 at this time, or use v5 at your own risk.</p>

<p>If you use hdWGCNA in your research, please cite the following papers in addition to the original WGCNA publication:</p>

<ul>

<li><a href="https://www.cell.com/cell-reports-methods/fulltext/S2667-2375(23)00127-3" class="external-link">Morabito et al., Cell Reports Methods (2023)</a></li>

<ul class="list-unstyled">

<li><a href="https://github.com/smorabit/hdWGCNA/tree/dev" class="external-link"><img src="https://img.shields.io/github/r-package/v/smorabit/hdWGCNA" alt="R"></a></li>

<li><a href="https://github.com/smorabit/hdWGCNA/issues" class="external-link"><img src="https://img.shields.io/github/issues/smorabit/hdWGCNA" alt="ISSUES"></a></li>

<li><a href="https://www.biorxiv.org/content/10.1101/2022.09.22.509094v1" class="external-link"><img src="https://img.shields.io/badge/publication-bioRxiv-dodgerblue" alt="Publication"></a></li>

<li><a href="https://www.cell.com/cell-reports-methods/fulltext/S2667-2375(23)00127-3" class="external-link"><img src="https://img.shields.io/badge/publication-Cell%20Rep%20Meth-%2300A1D7" alt="Publication"></a></li>

<li><a href="https://github.com/smorabit/hdWGCNA" class="external-link"><img src="https://img.shields.io/badge/Lifecycle-Maturing-007EC6" alt="Lifecycle:Maturing"></a></li>

<li><a href="https://github.com/smorabit/hdWGCNA/" class="external-link"><img src="https://img.shields.io/github/stars/smorabit/hdWGCNA?style=social" alt="Stars"></a></li>

</ul>