scfurl / viewmaster

Viewmaster

---

Viewmaster is a method for performing unsupervised classification of single cells across datasets written for use in the R environment.

The inputs are cell_data_set objects (see http://github/trapnell-lab/monocle3)

Installation

1. Download ArrayFire: https://arrayfire.com/binaries/

2. Install in R

if (!requireNamespace("devtools", quietly = TRUE)) install.packages("devtools")

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


devtools::install_github("daqana/rcpparrayfire")
devtools::install_github("furlan-lab/viewmaster")

Example

query_cds <- viewmaster(query_cds, 
                      ref_cds, 
                      ref_celldata_col="celltype", 
                      query_celldata_col=NULL, 
                      FUNC=c("naive_bayes", "neural_network", "bagging","softmax_regression", "logistic_regression", "deep_belief_nn", "perceptron"),
                      selected_genes=NULL,
                      train_frac = 0.8,
                      verbose = T)

Acknowledgements

Written by Scott Furlan.