Measuring Cell Type Similarity with Gene Ontology in Single-Cell RNA-Seq.
scGOclust
Leveraging Gene Ontology to Measure Cell Type Similarity Between Single Cell RNA-Seq Datasets
Author & Maintainer: Yuyao Song [email protected]
Note main branch version is compatible with Seurat and SeuratObject >= V5.0. If you are still using V4.0, please go to release scGOclust_V0.1.3.
Installation
First create the conda environment. Mamba is recommended as a faster alternative for conda.
conda env create -f scGOclust_conda_7Dec2022.yml
Then, open R under this environment, and install several packages not in conda:
remotes::install_github('satijalab/seurat-wrappers'), install.packages("pheatmap", "slanter")
Finally, install
scGOclust
from GitHub:devtools::install_github("Papatheodorou-Group/scGOclust", ref = "main")
Usage
This package operates on pairs of Seurat
objects
Refer to vignettes
for usage examples