[](https://travis-ci.org/campbio/celda) [](https://coveralls.io/github/campbio/celda?branch=master) # 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/ **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)