scGOclust
Measuring Cell Type Similarity with Gene Ontology in Single-Cell RNA-Seq
Traditional methods for analyzing single cell RNA-seq datasets focus solely on gene expression, but this package introduces a novel approach that goes beyond this limitation. Using Gene Ontology terms as features, the package allows for the functional profile of cell populations, and comparison within and between datasets from the same or different species. Our approach enables the discovery of previously unrecognized functional similarities and differences between cell types and has demonstrated success in identifying cell types' functional correspondence even between evolutionarily distant species.
README
# scGOclust
## Leveraging Gene Ontology to Measure Cell Type Similarity Between Single Cell RNA-Seq Datasets
Author & Maintainer: Yuyao Song <ysong@ebi.ac.uk>
**Note** main branch version is compatible with [Seurat](https://CRAN.R-project.org/package=Seurat) and [SeuratObject](https://CRAN.R-project.org/package=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
Versions across snapshots
| Version | Repository | File | Size |
|---|---|---|---|
0.2.1 |
rolling linux/jammy R-4.5 | scGOclust_0.2.1.tar.gz |
3.4 MiB |
0.2.1 |
rolling linux/noble R-4.5 | scGOclust_0.2.1.tar.gz |
3.4 MiB |
0.2.1 |
rolling source/ R- | scGOclust_0.2.1.tar.gz |
3.4 MiB |
0.2.1 |
latest linux/jammy R-4.5 | scGOclust_0.2.1.tar.gz |
3.4 MiB |
0.2.1 |
latest linux/noble R-4.5 | scGOclust_0.2.1.tar.gz |
3.4 MiB |
0.2.1 |
latest source/ R- | scGOclust_0.2.1.tar.gz |
3.4 MiB |
0.2.1 |
2026-04-26 source/ R- | scGOclust_0.2.1.tar.gz |
3.4 MiB |
0.2.1 |
2026-04-23 source/ R- | scGOclust_0.2.1.tar.gz |
3.4 MiB |
0.2.1 |
2025-04-20 source/ R- | scGOclust_0.2.1.tar.gz |
3.4 MiB |