Science Score: 77.0%
This score indicates how likely this project is to be science-related based on various indicators:
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✓CITATION.cff file
Found CITATION.cff file -
✓codemeta.json file
Found codemeta.json file -
✓.zenodo.json file
Found .zenodo.json file -
✓DOI references
Found 12 DOI reference(s) in README -
✓Academic publication links
Links to: zenodo.org -
✓Committers with academic emails
2 of 6 committers (33.3%) from academic institutions -
○Institutional organization owner
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○JOSS paper metadata
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○Scientific vocabulary similarity
Low similarity (14.7%) to scientific vocabulary
Keywords
Repository
Single-cell data analysis
Basic Info
- Host: GitHub
- Owner: jhu99
- License: mit
- Language: Python
- Default Branch: main
- Homepage: https://scbean.readthedocs.io
- Size: 18.3 MB
Statistics
- Stars: 15
- Watchers: 3
- Forks: 4
- Open Issues: 1
- Releases: 6
Topics
Metadata Files
README.md
https://orcid.org/0000-0002-3351-8020
Scbean integrates a range of models for single-cell data analysis, including dimensionality reduction, remvoing batch effects, and transferring well-annotated cell type labels from scRNA-seq to scATAC-seq and spatial resoved transcriptomics. It is efficient and scalable for large-scale datasets. Scbean will also provide more fundamental analyses for multi-modal data and spatial resoved transcriptomics in the future. The output of our integrated data can be easily used for downstream data analyses such as clustering, identification of cell subpopulations, differential gene expression, visualization using either Seurat or Scanpy.
Four APIs for the analysis of multi-omics data
- DAVAE supports integration of scRNA-seq, scATAC-seq, spatial transcriptomics based on domain-adversarial and variational approximation.
- VIPCCA supports integration of unpaired single-cell multi-omics data, differential gene expression analysis based on non-linear canonical correlation analysis.
- VIMCCA supports joint-analysis of paired multimodal single-cell data based on multi-view latent variable model.
- VISGP supports the discovery of spatially variable genes exhibiting distinct expression patterns in spatial transcriptome data.
Citation
Haohui Zhang, Yuwei Wang, Bin Lian, Yiran Wang, Xingyi Li, Tao Wang, Xuequn Shang, Hui Yang, Ahmad Aziz, Jialu Hu, Scbean: a python library for single-cell multi-omics data analysis, Bioinformatics, 2024;, btae053, https://doi.org/10.1093/bioinformatics/btae053
Yuwei Wang, Bin Lian, Haohui Zhang, Yuanke Zhong, Jie He, Fashuai Wu, Knut Reinert, Xuequn Shang, Hui Yang, Jialu Hu, A multi-view latent variable model reveals cellular heterogeneity in complex tissues for paired multimodal single-cell data, Bioinformatics, Volume 39, Issue 1, January 2023, btad005, https://doi.org/10.1093/bioinformatics/btad005
Jialu Hu, Mengjie Chen, Xiang Zhou, Effective and scalable single-cell data alignment with non-linear canonical correlation analysis, Nucleic Acids Research, Volume 50, Issue 4, 28 February 2022, Page e21, https://doi.org/10.1093/nar/gkab1147
Jialu Hu, Yuanke Zhong, Xuequn Shang, A versatile and scalable single-cell data integration algorithm based on domain-adversarial and variational approximation, Briefings in Bioinformatics, Volume 23, Issue 1, January 2022, bbab400, https://doi.org/10.1093/bib/bbab400
Jialu Hu, Yiran Wang, Xiang Zhou, and Mengjie Chen. "Pre-processing, Dimension Reduction, and Clustering for Single-Cell RNA-seq Data." In Handbook of Statistical Bioinformatics, pp. 37-51. Springer, Berlin, Heidelberg, 2022. https://doi.org/10.1007/978-3-662-65902-1_2
Installation
- Create conda environment
shell
$ conda create -n scbean python=3.8
$ conda activate scbean
- Install scbean from pypi
shell
$ pip install scbean
- Alternatively, install the develop version of scbean from GitHub source code
shell
$ git clone https://github.com/jhu99/scbean.git
$ cd ./scbean/
$ python -m pip install .
Note: Please make sure your python version >= 3.7, and install tensorflow-gpu if GPU is available on your your machine.
Usage of scbean
For a quick start, please follow our guide about the usage of scbean in the Tutorial and Documentation pages.
Owner
- Name: Jialu Hu
- Login: jhu99
- Kind: user
- Repositories: 5
- Profile: https://github.com/jhu99
Citation (CITATION.cff)
cff-version: 1.2.0
message: "If you use this software, please cite it as below."
authors:
- family-names: Hu
given-names: Jialu
orcid: https://orcid.org/0000-0002-3351-8020
title: "Scbean: a toolkit for integrating single-cell multimodal data"
version: 0.5.6
identifiers:
- type: doi
value: 10.5281/zenodo.10611941
date-released: 2024-02-02
GitHub Events
Total
- Watch event: 1
Last Year
- Watch event: 1
Committers
Last synced: 7 months ago
Top Committers
| Name | Commits | |
|---|---|---|
| Jialu Hu | j****u@n****n | 123 |
| HaoHuiZhang | 9****d | 72 |
| drizzlezyk | 4****k | 72 |
| wangyr997 | 6****7 | 47 |
| yuwei-star | 7****r | 17 |
| jhu | j****u@u****u | 1 |
Committer Domains (Top 20 + Academic)
Issues and Pull Requests
Last synced: 7 months ago
All Time
- Total issues: 2
- Total pull requests: 4
- Average time to close issues: 2 months
- Average time to close pull requests: 2 months
- Total issue authors: 2
- Total pull request authors: 3
- Average comments per issue: 2.0
- Average comments per pull request: 0.0
- Merged pull requests: 3
- Bot issues: 0
- Bot pull requests: 0
Past Year
- Issues: 0
- Pull requests: 0
- Average time to close issues: N/A
- Average time to close pull requests: N/A
- Issue authors: 0
- Pull request authors: 0
- Average comments per issue: 0
- Average comments per pull request: 0
- Merged pull requests: 0
- Bot issues: 0
- Bot pull requests: 0
Top Authors
Issue Authors
- oldvalley49 (1)
- liuchunlei0430 (1)
Pull Request Authors
- wangyr997 (2)
- jhu99 (1)
- drizzlezyk (1)
Top Labels
Issue Labels
Pull Request Labels
Packages
- Total packages: 2
-
Total downloads:
- pypi 107 last-month
-
Total dependent packages: 0
(may contain duplicates) -
Total dependent repositories: 2
(may contain duplicates) - Total versions: 21
- Total maintainers: 1
proxy.golang.org: github.com/jhu99/scbean
- Documentation: https://pkg.go.dev/github.com/jhu99/scbean#section-documentation
- License: mit
-
Latest release: v0.5.7
published about 2 years ago
Rankings
pypi.org: scbean
integration
- Homepage: https://github.com/jhu99/scbean
- Documentation: https://scbean.readthedocs.io/
- License: MIT
-
Latest release: 0.5.6
published about 2 years ago
Rankings
Maintainers (1)
Dependencies
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- Jinja2 ==2.11.2
- Keras ==2.3.0
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- Keras-Preprocessing ==1.1.2
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- nest-asyncio ==1.4.3
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- packaging ==20.8
- pandas ==1.1.0
- pandocfilters ==1.4.3
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- pexpect ==4.8.0
- pickleshare ==0.7.5
- prompt-toolkit ==3.0.10
- protobuf ==3.14.0
- ptyprocess ==0.7.0
- pyasn1 ==0.4.8
- pyasn1-modules ==0.2.8
- pyparsing ==2.4.7
- pyrsistent ==0.17.3
- python-dateutil ==2.8.1
- python-igraph ==0.8.2
- pytz ==2020.5
- pyzmq ==20.0.0
- recommonmark ==0.7.1
- requests ==2.25.1
- requests-oauthlib ==1.3.0
- rsa ==4.6
- scanpy ==1.6.0
- scbean ==0.2.6
- scikit-learn ==0.24.0
- scipy ==1.4.1
- seaborn ==0.11.1
- setuptools-scm ==5.0.1
- sinfo ==0.3.1
- six ==1.15.0
- snowballstemmer ==2.0.0
- sphinx-rtd-theme ==0.5.1
- sphinxcontrib-applehelp ==1.0.2
- sphinxcontrib-devhelp ==1.0.2
- sphinxcontrib-htmlhelp ==1.0.3
- sphinxcontrib-jsmath ==1.0.1
- sphinxcontrib-qthelp ==1.0.3
- sphinxcontrib-serializinghtml ==1.1.4
- statsmodels ==0.12.1
- stdlib-list ==0.8.0
- tables ==3.6.1
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- tensorboard-plugin-wit ==1.7.0
- tensorflow ==2.4.0
- tensorflow-estimator ==2.4.0
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- testpath ==0.4.4
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- threadpoolctl ==2.1.0
- tornado ==6.1
- tqdm ==4.55.1
- traitlets ==5.0.5
- typing-extensions ==3.7.4.3
- umap-learn ==0.4.6
- urllib3 ==1.26.2
- wcwidth ==0.2.5
- webencodings ==0.5.1
- wrapt ==1.12.1
- zipp ==3.4.0
- anndata *
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- keras ==2.3.1
- louvain *
- pandas *
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- scipy *
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- tensorflow ==2.4.0
- actions/checkout v2 composite
- IPython *
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- recommonmark *
- sphinx_rtd_theme *