https://github.com/theislab/atlas-feature-selection-benchmark
Code for "Feature selection methods affect the performance of scRNA-seq data integration and querying"
https://github.com/theislab/atlas-feature-selection-benchmark
benchmarking feature-selection integration scrna-seq
Last synced: 10 months ago
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Code for "Feature selection methods affect the performance of scRNA-seq data integration and querying"
- Host: GitHub
- URL: https://github.com/theislab/atlas-feature-selection-benchmark
- Owner: theislab
- License: mit
- Created: 2022-08-17T09:05:06.000Z (almost 4 years ago)
- Default Branch: main
- Last Pushed: 2024-11-25T17:28:09.000Z (over 1 year ago)
- Last Synced: 2024-12-30T12:46:51.676Z (over 1 year ago)
- Topics: benchmarking, feature-selection, integration, scrna-seq
- Language: Jupyter Notebook
- Homepage:
- Size: 65.7 MB
- Stars: 5
- Watchers: 2
- Forks: 0
- Open Issues: 0
-
Metadata Files:
- Readme: README.md
- License: LICENSE
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README
# Atlas feature selection benchmarking
[](https://doi.org/10.1038/s41592-025-02624-3)
[](https://doi.org/10.5281/zenodo.13995812)
[](https://doi.org/10.6084/m9.figshare.c.7521966)
This repository contains code for benchmarking the effect of feature selection on scRNA-seq atlas construction and use.
For more information please refer to the documentation on the [wiki](https://github.com/theislab/atlas-feature-selection-benchmark/wiki).
## Directory structure
* `analysis/` - Notebooks used to perform analysis of the results
* `R/` - R functions used in the analysis notebooks
* `bin/` - Scripts used in **Nextflow** workflows
* `functions/` - Functions used across multiple scripts
* `conf/` - **Nextflow** configuration files
* `data/` - Data files used in the analysis. Metric score files can downloaded from [figshare](https://figshare.com/articles/dataset/Metric_scores/26390911).
* `selected-features/` - Selected features files for each dataset. Can be downloaded from [figshare](https://figshare.com/articles/dataset/Selected_features/26390944).
* `envs/` - **conda** environment YAML files
* `output/` - Output from Nextflow workflows (not included in **git**)
* `reports/` - **RMarkdown** files and functions for output reports generated by the pipeline
* `work/` - The **Nextflow** working directory (not included in **git**)
* `workflows/` - **Nextflow** workflow files
* `LICENSE` - The project license
* `main.nf` - Main **Nextflow** workflow file
* `nextflow.config` - Main **Nextflow** config file
* `README.md` - This README
* `style_bin.sh` - A script for styling the files in `bin/`
## Data files
Data files for this project are available from [figshare](https://doi.org/10.6084/m9.figshare.c.7521966).
The analysis reports in the `analysis/` directory assume:
* [Metric files](https://figshare.com/articles/dataset/Metric_scores/26390911) are downloaded to the `data/` directory
* [Selected features files](https://figshare.com/articles/dataset/Selected_features/26390944) are downloaded to the `data/selected-features/` directory
## Citation
To refer to this repository, please cite:
> Zappia, L., Ramírez-Suástegui, C., Kfuri-Rubens, R., Vornholz, L., Wang, W., Dietrich, O., Frishberg, A., D Luecken, M. & J Theis, F. [_Feature selection methods affect the performance of scRNA-seq data integration and querying._](https://doi.org/10.1038/s41592-025-02624-3) Nature methods 1–11 (2025). doi:10.1038/s41592-025-02624-3
```bibtex
@ARTICLE{Zappia2025,
title = "{Feature selection methods affect the performance of scRNA-seq
data integration and querying}",
author = "Zappia, Luke and Richter, Sabrina and Ramírez-Suástegui, Ciro and
Kfuri-Rubens, Raphael and Vornholz, Larsen and Wang, Weixu and
Dietrich, Oliver and Frishberg, Amit and Luecken, Malte D and
Theis, Fabian J",
journal = "Nature methods",
publisher = "Nature Publishing Group",
pages = "1--11",
month = mar,
year = 2025,
doi = "10.1038/s41592-025-02624-3",
pmid = 40082610,
issn = "1548-7091,1548-7105",
language = "en"
}
```