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scarches

Reference mapping for single-cell genomics

https://github.com/theislab/scarches

Science Score: 54.0%

This score indicates how likely this project is to be science-related based on various indicators:

  • ○
    CITATION.cff file
  • ✓
    codemeta.json file
    Found codemeta.json file
  • ✓
    .zenodo.json file
    Found .zenodo.json file
  • ○
    DOI references
  • ✓
    Academic publication links
    Links to: nature.com
  • ✓
    Committers with academic emails
    5 of 37 committers (13.5%) from academic institutions
  • ✓
    Institutional organization owner
    Organization theislab has institutional domain (www.helmholtz-muenchen.de)
  • ○
    JOSS paper metadata
  • ○
    Scientific vocabulary similarity
    Low similarity (12.6%) to scientific vocabulary

Keywords

batch-correction data-integration deep-learning human-cell-atlas multimodal-deep-learning multiomics rna-seq-analysis scrna-seq single-cell single-cell-genomics

Keywords from Contributors

bioinformatics transcriptomics anndata scanpy scverse visualize-data
Last synced: 6 months ago · JSON representation

Repository

Reference mapping for single-cell genomics

Basic Info
Statistics
  • Stars: 382
  • Watchers: 11
  • Forks: 63
  • Open Issues: 62
  • Releases: 15
Topics
batch-correction data-integration deep-learning human-cell-atlas multimodal-deep-learning multiomics rna-seq-analysis scrna-seq single-cell single-cell-genomics
Created over 6 years ago · Last pushed 7 months ago
Metadata Files
Readme License

README.rst 

.. raw:: html

 

|PyPI| |PyPIDownloads| |Docs|


Single-cell architecture surgery (scArches) is a package for reference-based analysis of single-cell data.


What is scArches?
-------------------------------
scArches allows your single-cell query data to be analyzed by integrating it into a reference atlas. By mapping your data into an integrated reference you can transfer cell-type annotation from reference to query, identify disease states by mapping to healthy atlas, and advanced applications such as imputing missing data modalities or spatial locations.


Usage and installation
-------------------------------
See `here `_ for documentation and tutorials.

Support and contribute
-------------------------------
If you have a question or new architecture or a model that could be integrated into our pipeline, you can
post an `issue `__ or reach us by `email `_.

Reference
-------------------------------
If scArches is helpful in your research, please consider citing the following `paper `_:
::


       @article{lotfollahi2021mapping,
         title={Mapping single-cell data to reference atlases by transfer learning},
         author={Lotfollahi, Mohammad and Naghipourfar, Mohsen and Luecken, Malte D and Khajavi,
         Matin and B{\"u}ttner, Maren and Wagenstetter, Marco and Avsec, {\v{Z}}iga and Gayoso,
         Adam and Yosef, Nir and Interlandi, Marta and others},
         journal={Nature Biotechnology},
         pages={1--10},
         year={2021},
         publisher={Nature Publishing Group}}




.. |PyPI| image:: https://img.shields.io/pypi/v/scarches.svg
   :target: https://pypi.org/project/scarches

.. |PyPIDownloads| image:: https://pepy.tech/badge/scarches
   :target: https://pepy.tech/project/scarches

.. |Docs| image:: https://readthedocs.org/projects/scarches/badge/?version=latest
   :target: https://scarches.readthedocs.io

Owner

  • Name: Theis Lab
  • Login: theislab
  • Kind: organization
  • Email: icb.office@helmholtz-muenchen.de
  • Location: Munich

Institute of Computational Biology

GitHub Events

Total
  • Issues event: 23
  • Watch event: 41
  • Issue comment event: 42
  • Push event: 4
  • Pull request event: 1
  • Fork event: 11
Last Year
  • Issues event: 23
  • Watch event: 41
  • Issue comment event: 42
  • Push event: 4
  • Pull request event: 1
  • Fork event: 11

Committers

Last synced: over 2 years ago

All Time
  • Total Commits: 1,076
  • Total Committers: 37
  • Avg Commits per committer: 29.081
  • Development Distribution Score (DDS): 0.656
Past Year
  • Commits: 162
  • Committers: 17
  • Avg Commits per committer: 9.529
  • Development Distribution Score (DDS): 0.704
Top Committers
Name Email Commits
Mohsen Naghipourfar m****p@g****m 370
naghipourfar m****r@g****m 149
Koncopd k****d@g****m 125
M0hammadL 3****L 111
cdedonno c****o@h****e 62
marco m****r@t****e 40
m0hammadl m****i@h****e 37
aidinbii b****n@g****m 30
MohsenNaghipourfar 6****r 24
m0hammadl m****i@g****m 21
Aleksandra Topalova a****a@g****m 19
Matin Khajavi m****0@y****m 15
carlo.dedonno c****o@l****m 15
lcmmichielsen l****n@h****m 9
Amir Ali Moinfar a****r@h****e 6
LisaSikkema l****2@h****m 4
ICB Aleksandra Topalova a****a@h****e 4
ICB Anastasia Litinetskaya a****t@g****m 4
Amir Ali Moinfar m****i@g****m 4
Maren Büttner m****r@h****e 3
Marco Wagenstetter 4****5 3
EliHei2 5****2 3
ICB Mohsen Naghipourfar m****r@i****e 2
Maarten de Vries 3****s 2
Matin Khajavi 5****i 2
drEast f****t@h****e 1
Karin Hrovatin 4****n 1
Anastasia Litinetskaya a****t 1
natbutter n****r@g****m 1
ICB Aleksandra Topalova a****a@s****e 1
and 7 more...
Committer Domains (Top 20 + Academic)
helmholtz-muenchen.de: 5 posteo.net: 1 vicb-submit-02.scidom.de: 1 gpusrv10.scidom.de: 1 supergpu02pxe.scidom.de: 1 icb-gpusrv01.scidom.de: 1 hpc-submit01.scidom.de: 1 t-online.de: 1

Issues and Pull Requests

Last synced: 6 months ago

All Time
  • Total issues: 103
  • Total pull requests: 73
  • Average time to close issues: about 1 month
  • Average time to close pull requests: 13 days
  • Total issue authors: 83
  • Total pull request authors: 17
  • Average comments per issue: 2.63
  • Average comments per pull request: 1.53
  • Merged pull requests: 46
  • Bot issues: 0
  • Bot pull requests: 0
Past Year
  • Issues: 18
  • Pull requests: 1
  • Average time to close issues: 16 days
  • Average time to close pull requests: N/A
  • Issue authors: 17
  • Pull request authors: 1
  • Average comments per issue: 1.11
  • Average comments per pull request: 0.0
  • Merged pull requests: 0
  • Bot issues: 0
  • Bot pull requests: 0
View more stats
Top Authors
Issue Authors
  • melancholy12 (6)
  • chansigit (3)
  • Nusob888 (3)
  • LisaSikkema (3)
  • jasperhyp (2)
  • maarten-devries (2)
  • YawnC (2)
  • yojetsharma (2)
  • virpatel524 (2)
  • tvegawaichman (2)
  • jianrong0520 (2)
  • bitcometz (2)
  • Cicilalal (2)
  • DzvinkaYarish (1)
  • Niubile001 (1)
Pull Request Authors
  • chelseabright96 (14)
  • cdedonno (13)
  • lcmmichielsen (7)
  • maarten-devries (6)
  • moinfar (5)
  • alextopalova (4)
  • Koncopd (4)
  • M0hammadL (4)
  • DeepOzean (4)
  • EliHei2 (3)
  • alitinet (2)
  • MohammedZidane (2)
  • drEast (1)
  • LisaSikkema (1)
  • natbutter (1)
Top Labels
Issue Labels
enhancement (1)
Pull Request Labels

Packages

  • Total packages: 1
  • Total downloads:
    • pypi 1,306 last-month
  • Total dependent packages: 3
  • Total dependent repositories: 1
  • Total versions: 28
  • Total maintainers: 4
pypi.org: scarches

Transfer learning with Architecture Surgery on Single-cell data

  • Versions: 28
  • Dependent Packages: 3
  • Dependent Repositories: 1
  • Downloads: 1,306 Last month
Rankings
Dependent packages count: 3.2%
Stargazers count: 3.7%
Forks count: 6.0%
Downloads: 6.7%
Average: 8.2%
Dependent repos count: 21.5%
Maintainers (4)
naghipourfar Koncopd Cottoneyejoe m0hammadl
Last synced: 6 months ago

Dependencies

docs/requirements.txt pypi
  • cython *
  • ipykernel *
  • nbconvert >=5.6.1
  • nbsphinx >=0.7
  • numpydoc *
  • pkgconfig *
  • sphinx >=3.0.3
setup.py pypi
  • anndata >=0.7.4
  • gdown *
  • h5py >=2.10.0
  • matplotlib >=3.3.1
  • numpy >=1.19.2
  • pandas >=1.1.2
  • requests *
  • scHPL >=1.0.0
  • scanpy >=1.6.0
  • scikit-learn >=0.23.2
  • scipy >=1.5.2
  • scvi-tools >=0.12.1
  • torch >=1.8.0
  • tqdm >=4.56.0