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Open Source Science

https://github.com/cbg-ethz/scdef

Deep exponential families for single-cell data.

https://github.com/cbg-ethz/scdef

Science Score: 36.0%

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
  • ✓
    Committers with academic emails
    1 of 2 committers (50.0%) from academic institutions
  • ○
    Institutional organization owner
  • ○
    JOSS paper metadata
  • ○
    Scientific vocabulary similarity
    Low similarity (8.2%) to scientific vocabulary

Keywords

batch-integration gene-signatures hierarchical-models jax matrix-factorization scrna-seq single-cell-rna-seq variational-inference
Last synced: 5 months ago · JSON representation

Repository

Deep exponential families for single-cell data.

Basic Info
Statistics
  • Stars: 20
  • Watchers: 4
  • Forks: 1
  • Open Issues: 0
  • Releases: 1
Topics
batch-integration gene-signatures hierarchical-models jax matrix-factorization scrna-seq single-cell-rna-seq variational-inference
Created over 3 years ago · Last pushed over 1 year ago
Metadata Files
Readme

README.md

pypi build docs

Deep exponential families for single-cell data. scDEF learns hierarchies of cell states and their gene signatures from scRNA-seq data. The method can be used for dimensionality reduction, visualization, gene signature identification, clustering at multiple levels of resolution, and batch integration. The informed version (iscDEF) can additionally take known gene lists to jointly assign cells to types and find clusters within each type.

To install scDEF and get started, read the documentation.

Owner

  • Name: Computational Biology Group (CBG)
  • Login: cbg-ethz
  • Kind: organization
  • Location: Basel, Switzerland

Beerenwinkel Lab at ETH Zurich

GitHub Events

Total
  • Watch event: 1
  • Push event: 44
  • Pull request event: 4
  • Create event: 1
Last Year
  • Watch event: 1
  • Push event: 44
  • Pull request event: 4
  • Create event: 1

Committers

Last synced: 10 months ago

All Time
  • Total Commits: 437
  • Total Committers: 2
  • Avg Commits per committer: 218.5
  • Development Distribution Score (DDS): 0.016
Past Year
  • Commits: 99
  • Committers: 2
  • Avg Commits per committer: 49.5
  • Development Distribution Score (DDS): 0.071
Top Committers
Name Email Commits
pedrofale p****a@b****h 430
NBMueller n****r@w****e 7
Committer Domains (Top 20 + Academic)
bsse.ethz.ch: 1

Issues and Pull Requests

Last synced: 6 months ago

All Time
  • Total issues: 1
  • Total pull requests: 11
  • Average time to close issues: about 1 month
  • Average time to close pull requests: about 18 hours
  • Total issue authors: 1
  • Total pull request authors: 2
  • Average comments per issue: 1.0
  • Average comments per pull request: 0.18
  • Merged pull requests: 9
  • Bot issues: 0
  • Bot pull requests: 0
Past Year
  • Issues: 1
  • Pull requests: 10
  • Average time to close issues: about 1 month
  • Average time to close pull requests: about 20 hours
  • Issue authors: 1
  • Pull request authors: 2
  • Average comments per issue: 1.0
  • Average comments per pull request: 0.2
  • Merged pull requests: 8
  • Bot issues: 0
  • Bot pull requests: 0
View more stats
Top Authors
Issue Authors
  • pedrofale (1)
Pull Request Authors
  • pedrofale (16)
  • NBMueller (3)
Top Labels
Issue Labels
Pull Request Labels

Packages

  • Total packages: 1
  • Total downloads:
    • pypi 62 last-month
  • Total dependent packages: 0
  • Total dependent repositories: 0
  • Total versions: 33
  • Total maintainers: 1
pypi.org: scdef

Extract hierarchical signatures of cell state from single-cell data.

  • Versions: 33
  • Dependent Packages: 0
  • Dependent Repositories: 0
  • Downloads: 62 Last month
Rankings
Dependent packages count: 7.3%
Average: 24.3%
Dependent repos count: 41.3%
Maintainers (1)
pedrofale
Last synced: 6 months ago

Dependencies

.github/workflows/docs.yaml actions
  • actions/cache v2 composite
  • actions/checkout v2 composite
  • actions/setup-python v2 composite
  • snok/install-poetry v1 composite
.github/workflows/test.yaml actions
  • actions/checkout v2 composite
  • actions/setup-python v2 composite
  • pypa/gh-action-pypi-publish master composite
  • snok/install-poetry v1 composite
  • ts-graphviz/setup-graphviz v1 composite
pyproject.toml pypi
  • black ^23.3.0 develop
  • bump2version ^1.0.1 develop
  • jupyter_contrib_nbextensions ^0.7.0 develop
  • mkdocs ^1.4.3 develop
  • mkdocs-jupyter ^0.24.2 develop
  • mkdocs-material ^9.1.18 develop
  • mkdocstrings ^0.22.0 develop
  • notebook ~6.0.0 develop
  • pytest ^6.2.4 develop
  • anndata ^0.9.2
  • click ^8.0.1
  • graphviz ^0.14.2
  • gseapy ^1.0.4
  • igraph ^0.10.4
  • jax >=0.4.13
  • jaxlib >=0.4.13
  • numba ~0.56.0
  • numpy ^1.23.4
  • pandas ^1.5.1
  • python >=3.8,<4.0
  • scanpy ^1.9.5
  • tqdm ^4.64.0