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scGOclust

Leveraging Gene Ontology to Measure Cell Type Similarity Between Single Cell RNA-Seq Datasets

Author & Maintainer: Yuyao Song [email protected]

cran downloads

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

  1. First create the conda environment. Mamba is recommended as a faster alternative for conda.

    conda env create -f scGOclust_conda_7Dec2022.yml

  2. Then, open R under this environment, and install several packages not in conda:

    remotes::install_github('satijalab/seurat-wrappers'), install.packages("pheatmap", "slanter")

  3. 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

License: GPLv3.0

Citation

Please cite our preprint or the CRAN package.