cellassign
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Automated, probabilistic assignment of cell types in scRNA-seq data
cellassign
cellassign
automatically assigns single-cell RNA-seq data to known cell types across thousands of cells accounting for patient and batch specific effects. Information about a priori known markers cell types is provided as input to the model in the form of a (binary) marker gene by cell-type matrix. cellassign
then probabilistically assigns each cell to a cell type, removing subjective biases from typical unsupervised clustering workflows.
![](https://github.com/Irrationone/cellassign/raw/master/inst/cellassign_schematic.png)
Getting started
Installation
Installing from GitHub
cellassign
is built using Google's Tensorflow, and as such requires installation of the R package tensorflow
:
install.packages("tensorflow")
tensorflow::install_tensorflow(extra_packages='tensorflow-probability', version = "2.1.0")
Please ensure this installs version 2 of tensorflow. You can check this by calling
tensorflow::tf_config()
TensorFlow v2.1.0 (/usr/local/lib/python3.7/site-packages/tensorflow)
cellassign
can then be installed from github:
install.packages("devtools") # If not already installed
devtools::install_github("Irrationone/cellassign")
Installing from conda
With conda, install the current release version of cellassign
as follows:
conda install -c conda-forge -c bioconda r-cellassign
Documentation
Package documentation can be found here. This includes the following vignettes:
Basic usage
cellassign
requires the following inputs:
-
exprs_obj
: Cell-by-gene matrix of raw counts (or SingleCellExperiment withcounts
assay) -
marker_gene_info
: Binary gene-by-celltype marker gene matrix or list relating cell types to marker genes -
s
: Size factors -
X
: Design matrix for any patient/batch specific effects
The model can be run as follows:
cas <- cellassign(exprs_obj = gene_expression_data,
marker_gene_info = marker_gene_info,
s = s,
X = X)
An example set of markers for the human tumour microenvironment can be loaded by calling
data(example_TME_markers)
Please see the package vignette for details and caveats.
Paper
Code of Conduct
Please note that the 'cellassign' project is released with a Contributor Code of Conduct. By contributing to this project, you agree to abide by its terms.
Authors
Allen W Zhang, University of British Columbia
Kieran R Campbell, University of British Columbia