scperturb
scPerturb: A resource and a python/R tool for single-cell perturbation data
Science Score: 46.0%
This score indicates how likely this project is to be science-related based on various indicators:
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○CITATION.cff file
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✓codemeta.json file
Found codemeta.json file -
✓.zenodo.json file
Found .zenodo.json file -
○DOI references
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✓Academic publication links
Links to: nature.com, zenodo.org -
✓Committers with academic emails
6 of 9 committers (66.7%) from academic institutions -
○Institutional organization owner
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○JOSS paper metadata
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○Scientific vocabulary similarity
Low similarity (16.9%) to scientific vocabulary
Keywords
Repository
scPerturb: A resource and a python/R tool for single-cell perturbation data
Basic Info
- Host: GitHub
- Owner: sanderlab
- License: other
- Language: Jupyter Notebook
- Default Branch: master
- Homepage: http://www.sanderlab.org/scPerturb/
- Size: 209 MB
Statistics
- Stars: 139
- Watchers: 5
- Forks: 9
- Open Issues: 12
- Releases: 5
Topics
Metadata Files
README.md
scPerturb: A resource and a python tool for single-cell perturbation data
For the publication see: Peidli, S., Green, T.D., et al. Nature Methods (2024).
Where to find the data
The datasets are available to download on scperturb.org (where you can also find an interactive table of all included datasets). The latest versions are available in full on Zenodo, depending on the modality you are interested in: - RNA data - ATAC data
Most datasets are also downloadable via pertpy or Lamin.
scperturb for python (integrates with scanpy)
A python package to compute E-distances in single-cell perturbation data and perform E-tests.
Please note that maintenance on the scperturb Python package is relatively slow. We have recreated Python functionality in pertpy which has a larger base of support and also includes fast calculation of alternative distance metrics and tests.
Install
Just install via pip:
pip install scperturb
Usage example
Check out this notebook for a tutorial. Basic usage is: ```
E-distances
estats = edist(adata, obs_key='perturbation')
E-distances to a specific group (e.g. 'control')
estats_control = estats.loc['control']
E-test for difference to control
df = etest(adata, obskey='perturbation', obsmkey='X_pca', dist='sqeuclidean', control='control', alpha=0.05, runs=100) ```
scperturbR for R (integrates with Seurat)
We wrote an R version of scperturb that works with Seurat objects. You can find it as scperturbR on CRAN. A basic usage vignette is WIP.
Install using:
install.packages('scperturbR')
Reproducibility
Instructions to run the code to reproduce the figures and tables in the paper and supplement: - install conda if necessary (also check out mamba, it's way faster) - run "conda env create -f scenv.yaml" to create a new conda environment with all the necessary packages to run the code (you will need this) - activate the environment with "conda activate scenv" - download all the datasets from scperturb.org - in "config.yaml", change paths, especially the one to the directory where the data was downloaded to - run the notebooks in "notebooks" to produce the figures and tables found in the paper / supplement and the website (each saved to a different folder)
Owner
- Name: sanderlab
- Login: sanderlab
- Kind: organization
- Repositories: 6
- Profile: https://github.com/sanderlab
GitHub Events
Total
- Issues event: 7
- Watch event: 32
- Issue comment event: 2
- Push event: 2
- Fork event: 2
Last Year
- Issues event: 7
- Watch event: 32
- Issue comment event: 2
- Push event: 2
- Fork event: 2
Committers
Last synced: 9 months ago
Top Committers
| Name | Commits | |
|---|---|---|
| peidli | s****i@g****m | 106 |
| Tessa Green | t****n@g****u | 29 |
| cannin | c****n@g****m | 6 |
| Torsten Gross | g****1@g****m | 2 |
| judyueshen | c****n@g****u | 1 |
| tessadgreen | t****5@t****u | 1 |
| tessadgreen | t****5@l****u | 1 |
| tessadgreen | t****5@l****u | 1 |
| tessadgreen | t****5@l****u | 1 |
Committer Domains (Top 20 + Academic)
Issues and Pull Requests
Last synced: 6 months ago
All Time
- Total issues: 30
- Total pull requests: 1
- Average time to close issues: 4 months
- Average time to close pull requests: about 12 hours
- Total issue authors: 22
- Total pull request authors: 1
- Average comments per issue: 0.93
- Average comments per pull request: 0.0
- Merged pull requests: 1
- Bot issues: 0
- Bot pull requests: 0
Past Year
- Issues: 6
- Pull requests: 0
- Average time to close issues: about 19 hours
- Average time to close pull requests: N/A
- Issue authors: 6
- Pull request authors: 0
- Average comments per issue: 0.33
- Average comments per pull request: 0
- Merged pull requests: 0
- Bot issues: 0
- Bot pull requests: 0
Top Authors
Issue Authors
- stefanpeidli (7)
- tessadgreen (2)
- siduanmiao (2)
- FarzanT (2)
- Yonggie (1)
- kaiu85 (1)
- rootze (1)
- zhan8855 (1)
- deto (1)
- mksingh2104 (1)
- caodudu (1)
- mdanb (1)
- AstreChen (1)
- Gesmira (1)
- cyunhu (1)
Pull Request Authors
- GrossTor (1)
Top Labels
Issue Labels
Pull Request Labels
Packages
- Total packages: 2
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Total downloads:
- pypi 182 last-month
- cran 173 last-month
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Total dependent packages: 0
(may contain duplicates) -
Total dependent repositories: 0
(may contain duplicates) - Total versions: 8
- Total maintainers: 2
pypi.org: scperturb
Python package with E-distance tools for single-cell perturbation data analysis.
- Homepage: https://github.com/sanderlab/scPerturb
- Documentation: https://scperturb.readthedocs.io/
- License: MIT License
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Latest release: 0.1.0
published about 2 years ago
Rankings
Maintainers (1)
cran.r-project.org: scperturbR
E-Statistics for Seurat Objects
- Homepage: https://github.com/sanderlab/scPerturb/tree/master/package_r
- Documentation: http://cran.r-project.org/web/packages/scperturbR/scperturbR.pdf
- License: MIT + file LICENSE
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Latest release: 0.1.0
published almost 3 years ago
Rankings
Maintainers (1)
Dependencies
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- actions/deploy-pages v1 composite
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