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 # celda: CEllular Latent Dirichlet Allocation
 

 "celda" stands for "**CE**llular **L**atent **D**irichlet **A**llocation". It is a suite of Bayesian hierarchical models and supporting functions to perform gene and cell clustering for count data generated by single cell RNA-seq platforms. This algorithm is an extension of the Latent Dirichlet Allocation (LDA) topic modeling framework that has been popular in text mining applications. This package also includes a method called **DecontX** which can be used to estimate and remove contamination in single cell genomic data. 

 
 
 ## Installation Instructions
 

 To install the latest stable release of **celda** from [Bioconductor](http://bioconductor.org/packages/celda/) (requires R version >= 3.6):
 
 ```
 if (!requireNamespace("BiocManager", quietly = TRUE))
     install.packages("BiocManager")
 BiocManager::install("celda")
 ```
 
 To install the development version (R >= 3.6) of **celda** from GitHub using `devtools`:

 ```

 library(devtools)

 install_github("campbio/celda")

 ```

 **NOTE** For MAC OSX users, `devtools::install_github()` requires installation of **libgit2.** This can be installed via homebrew:

 ```

 brew install libgit2

 ```
 

 Also, if you receive installation errors when Rcpp is being installed and compiled, try following the steps outlined here to solve the issue:
 
 https://thecoatlessprofessor.com/programming/cpp/r-compiler-tools-for-rcpp-on-macos/

 If you are running R 4.0.0 or later version on MacOS Catalina and you see error `'wchar.h' file not found`, you can try the method in this link:
 
 https://discourse.mc-stan.org/t/dealing-with-catalina-iii/12731/5
 

 **NOTE** If you are trying to install **celda** using Rstudio and get this error: `could not find tools necessary to compile a package`, you can try this:

 ```
 options(buildtools.check = function(action) TRUE)
 ```

 ## Vignettes and examples

 To build the vignettes for Celda and DecontX during installation from GitHub, use the following command:
 
 ```
 library(devtools)
 install_github("campbio/celda", build_vignettes = TRUE)
 ```

 Note that installation may take an extra 5-10 minutes for building of the vignettes. The Celda and DecontX vignettes can then be accessed via the following commands:
 ```
 vignette("celda")
 vignette("decontX")
 ```

 
 ## For developers

 Check out our [Wiki](https://github.com/campbio/celda/wiki) for developer's guide if you want to contribute!
 - [Celda Development Coding Style Guide](https://github.com/campbio/celda/wiki/Celda-Development-Coding-Style-Guide)
 - [Celda Development Robust and Efficient Code](https://github.com/campbio/celda/wiki/Celda-Development-Robust-and-Efficient-Code)
 - [Celda Development Rstudio configuration](https://github.com/campbio/celda/wiki/Celda-Development-Rstudio-configuration)
 - [FAQ on how to use celda](https://github.com/campbio/celda/wiki/FAQ-on-how-to-use-celda)
 - [FAQ on package development](https://github.com/campbio/celda/wiki/FAQ-on-package-development)