Commit b25162e7 authored by smorabit's avatar smorabit
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updated website

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README.md

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scWGCNA is an R package for performing [weighted gene co-expression network analysis (WGCNA)](https://horvath.genetics.ucla.edu/html/CoexpressionNetwork/Rpackages/WGCNA/) in single-cell

RNA-seq data. scWGCNA constructs co-expression networks in a cell-type-specific manner,

identifies robust modules of highly inerconnected genes, and provides biological

context for these modules. For ease of use, scWGCNA is directly compatible with

[Seurat](https://satijalab.org/seurat/index.html) objects, one of the most common

formats for single-cell data.

identifies robust modules of inerconnected genes, and provides biological

context for these modules. scWGCNA is directly compatible with

[Seurat](https://satijalab.org/seurat/index.html) objects, one of the most ubiquitous

formats for single-cell data. Check out the [scWGCNA basics tutorial](articles/basic_tutorial.html) to get started.





## Installation
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We recommend creating an R [conda environment](https://docs.conda.io/en/latest/)

environment for scWGCNA.



```

```bash

# create new conda environment for R

conda create -n scWGCNA -c conda-forge r-base r-essentials

```



# activate conda environment

conda activate scWGCNA

```

install.packages('WGCNA')

install.packages('igraph')

install.packages('devtools')



# install Seurat, check their website for the most up-to-date instructions

install.packages('Seurat')

```

Next, open up R and install the required dependencies:



## Installation

* [Bioconductor](https://www.bioconductor.org/), an R-based software ecosystem for bioinformatics and biostatistics.

* [Seurat](https://satijalab.org/seurat/index.html), a general-purpose toolkit for single-cell data science.

* [WGCNA](https://horvath.genetics.ucla.edu/html/CoexpressionNetwork/Rpackages/WGCNA/), a package for co-expression network analysis.

* [igraph](https://igraph.org/r/), a package for general network analysis and visualization.

* [devtools](https://devtools.r-lib.org/), a package for package development in R.



Now you can install the scWGCNA package using `devtools`:

```r

# install BiocManager

install.packages("BiocManager")



# install Bioconductor core packages

BiocManager::install()



# install additional packages:

install.packages(c("Seurat", "WGCNA", "igraph", "devtools"))



```

devtools::install_github('smorabit/scWGCNA')



Now you can install the scWGCNA package using `devtools`. We are planning to add scWGCNA to CRAN and Bioconductor upon the 1.0 release in the next couple of months.



```r

devtools::install_github('smorabit/scWGCNA', branch='dev')

```

_pkgdown.yml

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  Samuel Morabito:

    href: https://smorabit.github.io



navbar:

 components:

   articles:

- title: scWGCNA Basics

  navbar: ~

  contents: basic_tutorial

- title: Network Visualization

  navbar: ~

  contents: network_visualizations

- title: Enrichment Analysis

  navbar: ~

  contents: enrichment_analysis

- title: Module Trait Correlation

  navbar: ~

  contents: module_trait_correlation

- title: Projecting Modules

  navbar: ~

  contents: projecting_modules

- title: Motif Analysis

  navbar: ~

  contents: motif_analysis

- title: Consensus WGCNA

  navbar: ~

  contents: consensus_wgcna

    text: Articles

    menu:

    - text: Core functionality

    - text: scWGCNA basics

      href: articles/basic_tutorial.html

    - text: Network visualization

      href: articles/network_visualizations.html

    - text: -------

    - text: Biological context for co-expression modules

    - text: Module trait correlation

      href: articles/module_trait_correlation.html

    - text: Enrichment analysis

      href: articles/enrichment_analysis.html

    - text: -------

    - text: Advanced topics

    - text: Consensus WGCNA

      href: articles/consensus_wgcna.html

    - text: Motif analysis

      href: articles/motif_analysis.html

    - text: Projecting modules onto new datasets

      href: articles/projecting_modules.html

    - text: -------

    - text: All articles

      href: articles/index.html







reference:

- title: Metacells

  desc: Functions for constructing metacells from single-cell data

docs/404.html

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<li class="nav-item dropdown">

  <a href="https://smorabit.github.io/scWGCNA/#" class="nav-link dropdown-toggle" data-bs-toggle="dropdown" role="button" aria-expanded="false" aria-haspopup="true" id="dropdown-articles">Articles</a>

  <div class="dropdown-menu" aria-labelledby="dropdown-articles">

    <a class="dropdown-item" href="https://smorabit.github.io/scWGCNA/articles/basic_tutorial.html">scWGCNA Basics</a>

    <a class="dropdown-item" href="https://smorabit.github.io/scWGCNA/articles/network_visualizations.html">scWGCNA Basics</a>

    <a class="dropdown-item" href="https://smorabit.github.io/scWGCNA/articles/enrichment_analysis.html">scWGCNA Basics</a>

    <a class="dropdown-item" href="https://smorabit.github.io/scWGCNA/articles/module_trait_correlation.html">Module Trait Correlation</a>

    <a class="dropdown-item" href="https://smorabit.github.io/scWGCNA/articles/projecting_modules.html">scWGCNA Basics</a>

    <a class="dropdown-item" href="https://smorabit.github.io/scWGCNA/articles/motif_analysis.html">Motif Analysis</a>

    <h6 class="dropdown-header" data-toc-skip>Core functionality</h6>

    <a class="dropdown-item" href="https://smorabit.github.io/scWGCNA/articles/basic_tutorial.html">scWGCNA basics</a>

    <a class="dropdown-item" href="https://smorabit.github.io/scWGCNA/articles/network_visualizations.html">Network visualization</a>

    <div class="dropdown-divider"></div>

    <h6 class="dropdown-header" data-toc-skip>Biological context for co-expression modules</h6>

    <a class="dropdown-item" href="https://smorabit.github.io/scWGCNA/articles/module_trait_correlation.html">Module trait correlation</a>

    <a class="dropdown-item" href="https://smorabit.github.io/scWGCNA/articles/enrichment_analysis.html">Enrichment analysis</a>

    <div class="dropdown-divider"></div>

    <h6 class="dropdown-header" data-toc-skip>Advanced topics</h6>

    <a class="dropdown-item" href="https://smorabit.github.io/scWGCNA/articles/consensus_wgcna.html">Consensus WGCNA</a>

    <a class="dropdown-item" href="https://smorabit.github.io/scWGCNA/articles/motif_analysis.html">Motif analysis</a>

    <a class="dropdown-item" href="https://smorabit.github.io/scWGCNA/articles/projecting_modules.html">Projecting modules onto new datasets</a>

    <div class="dropdown-divider"></div>

    <a class="dropdown-item" href="https://smorabit.github.io/scWGCNA/articles/index.html">All articles</a>

  </div>

</li>

      </ul>

docs/LICENSE-text.html

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<li class="nav-item dropdown">

  <a href="#" class="nav-link dropdown-toggle" data-bs-toggle="dropdown" role="button" aria-expanded="false" aria-haspopup="true" id="dropdown-articles">Articles</a>

  <div class="dropdown-menu" aria-labelledby="dropdown-articles">

    <a class="dropdown-item" href="articles/basic_tutorial.html">scWGCNA Basics</a>

    <a class="dropdown-item" href="articles/network_visualizations.html">scWGCNA Basics</a>

    <a class="dropdown-item" href="articles/enrichment_analysis.html">scWGCNA Basics</a>

    <a class="dropdown-item" href="articles/module_trait_correlation.html">Module Trait Correlation</a>

    <a class="dropdown-item" href="articles/projecting_modules.html">scWGCNA Basics</a>

    <a class="dropdown-item" href="articles/motif_analysis.html">Motif Analysis</a>

    <h6 class="dropdown-header" data-toc-skip>Core functionality</h6>

    <a class="dropdown-item" href="articles/basic_tutorial.html">scWGCNA basics</a>

    <a class="dropdown-item" href="articles/network_visualizations.html">Network visualization</a>

    <div class="dropdown-divider"></div>

    <h6 class="dropdown-header" data-toc-skip>Biological context for co-expression modules</h6>

    <a class="dropdown-item" href="articles/module_trait_correlation.html">Module trait correlation</a>

    <a class="dropdown-item" href="articles/enrichment_analysis.html">Enrichment analysis</a>

    <div class="dropdown-divider"></div>

    <h6 class="dropdown-header" data-toc-skip>Advanced topics</h6>

    <a class="dropdown-item" href="articles/consensus_wgcna.html">Consensus WGCNA</a>

    <a class="dropdown-item" href="articles/motif_analysis.html">Motif analysis</a>

    <a class="dropdown-item" href="articles/projecting_modules.html">Projecting modules onto new datasets</a>

    <div class="dropdown-divider"></div>

    <a class="dropdown-item" href="articles/index.html">All articles</a>

  </div>

</li>

      </ul><form class="form-inline my-2 my-lg-0" role="search">

docs/LICENSE.html

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<li class="nav-item dropdown">

  <a href="#" class="nav-link dropdown-toggle" data-bs-toggle="dropdown" role="button" aria-expanded="false" aria-haspopup="true" id="dropdown-articles">Articles</a>

  <div class="dropdown-menu" aria-labelledby="dropdown-articles">

    <a class="dropdown-item" href="articles/basic_tutorial.html">scWGCNA Basics</a>

    <a class="dropdown-item" href="articles/network_visualizations.html">scWGCNA Basics</a>

    <a class="dropdown-item" href="articles/enrichment_analysis.html">scWGCNA Basics</a>

    <a class="dropdown-item" href="articles/module_trait_correlation.html">Module Trait Correlation</a>

    <a class="dropdown-item" href="articles/projecting_modules.html">scWGCNA Basics</a>

    <a class="dropdown-item" href="articles/motif_analysis.html">Motif Analysis</a>

    <h6 class="dropdown-header" data-toc-skip>Core functionality</h6>

    <a class="dropdown-item" href="articles/basic_tutorial.html">scWGCNA basics</a>

    <a class="dropdown-item" href="articles/network_visualizations.html">Network visualization</a>

    <div class="dropdown-divider"></div>

    <h6 class="dropdown-header" data-toc-skip>Biological context for co-expression modules</h6>

    <a class="dropdown-item" href="articles/module_trait_correlation.html">Module trait correlation</a>

    <a class="dropdown-item" href="articles/enrichment_analysis.html">Enrichment analysis</a>

    <div class="dropdown-divider"></div>

    <h6 class="dropdown-header" data-toc-skip>Advanced topics</h6>

    <a class="dropdown-item" href="articles/consensus_wgcna.html">Consensus WGCNA</a>

    <a class="dropdown-item" href="articles/motif_analysis.html">Motif analysis</a>

    <a class="dropdown-item" href="articles/projecting_modules.html">Projecting modules onto new datasets</a>

    <div class="dropdown-divider"></div>

    <a class="dropdown-item" href="articles/index.html">All articles</a>

  </div>

</li>

      </ul><form class="form-inline my-2 my-lg-0" role="search">

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