vignettes/articles/installation.Rmd
installation.Rmd
“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.
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
'wchar.h' file not found
, you can try the method in this link:could not find tools necessary to compile a package
, you can try typing this before running the install command:options(buildtools.check = function(action) TRUE)