added dev badges, changelog, changed the logo

# scWGCNA 0.1.0 (2022-02-17)

## Added

- A lot of stuff oh wow.

## Changes

- Nothing

# scWGCNA 0.0.0.9000 (2021-07-15)

- The original (and now unsupported) version of scWGCNA included released in [Nature Genetics paper](https://doi.org/10.1038/s41588-021-00894-z).

GetModulePreservation <- function(seurat_obj, mod_name, wgcna_name=NULL){

  if(is.null(wgcna_name)){wgcna_name <- seurat_obj@misc$active_wgcna}

  if(is.null(seurat_obj@misc[[wgcna_name]]$module_preservation[[mod_name]])){

    stop("Invalid module preservation name.")

  }

  seurat_obj@misc[[wgcna_name]]$module_preservation[[mod_name]]

}

  if(is.null(wgcna_name)){wgcna_name <- seurat_obj@misc$active_wgcna}

  # get the module preservation stats:

  mod_pres <- GetModulePreservation(seurat_obj, name, wgcna_name)

  obs_df <- mod_pres$obs

  if(statistics == 'summary'){

    stat_list <- c("medianRank.pres", "Zsummary.pres")

  } else if(statistics == 'all'){

    stat_list <- c(colnames(obs_df[,-1]), colnames(Z_df[,-1]))

    stat_list <- c(colnames(obs_df[,-1])[grepl("Rank", colnames(obs_df[,-1]))], colnames(Z_df[,-1]))

  } else{

    stat_list <- statistics

  }

# scWGCNA <img src="man/figures/logo.png" align="right" height="20%" width="20%" />

[![R](https://img.shields.io/github/r-package/v/smorabit/scWGCNA)](https://github.com/smorabit/scWGCNA/tree/dev)

[![LICENSE](https://img.shields.io/github/license/smorabit/scWGCNA)](LICENSE.md)

[![ISSUES](https://img.shields.io/github/issues/smorabit/scWGCNA)](https://github.com/smorabit/scWGCNA/issues)

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 inerconnected genes, and provides biological

home:

  title: scWGCNA

  sidebar:

    structure: [license, citation, authors, dev]

authors:

  Samuel Morabito:

    href: https://smorabit.github.io

navbar:

  structure:

    left: [intro, articles, reference, news]

    right: [search, github]

  components:

   intro:

     text: Get started

     href: articles/scWGCNA.html

   news:

     text: News

     href: news/index.html

   articles:

    text: Vignettes

    menu:

    - text: All vignettes

      href: articles/index.html

reference:

- title: Metacells

  desc: Functions for constructing metacells from single-cell data