irzamsarfraz / celda

Bayesian Hierarchical Modeling for Clustering Single Cell Genomic Data

celda: CEllular Latent Dirichlet Allocation

"celda" stands for "CEllular Latent Dirichlet Allocation". 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 (requires R version >= 3.6):

if (!requireNamespace("BiocManager", quietly = TRUE))
    install.packages("BiocManager")
BiocManager::install("celda")

The latest stable version of celda can be installed from GitHub using devtools:

library(devtools)
install_github("campbio/celda")

The development version of celda can also be installed from GitHub using devtools:

library(devtools)
install_github("campbio/celda@devel")

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

If you are trying to install on MacOS in an Apple Silicon computater and you see the following error:

ld: warning: directory not found for option '-L/opt/gfortran/lib/gcc/x86_64-apple-darwin20.0/12.2.0'
ld: warning: directory not found for option '-L/opt/gfortran/lib'
ld: library not found for -lgfortran
clang: error: linker command failed with exit code 1 (use -v to see invocation)
make: *** [celda.so] Error 1
ERROR: compilation failed for package ‘celda’

You can solve this by downloading and installing the gfortran pkg located here and then running the following command:

sudo /opt/gfortran/bin/gfortran-update-sdk

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 for developer's guide if you want to contribute!

• Celda Development Coding Style Guide
• Celda Development Robust and Efficient Code
• Celda Development Rstudio configuration
• FAQ on how to use celda
• FAQ on package development