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GitHub / parashardhapola / scarf
Toolkit for highly memory efficient analysis of single-cell RNA-Seq, scATAC-Seq and CITE-Seq data. Analyze atlas scale datasets with millions of cells on laptop.
JSON API: https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/parashardhapola%2Fscarf
Stars: 89
Forks: 12
Open Issues: 10
License: bsd-3-clause
Language: Python
Repo Size: 32.6 MB
Dependencies:
57
Created: about 4 years ago
Updated: 25 days ago
Last pushed: 4 months ago
Last synced: 22 days ago
Commit Stats
Commits: 896
Authors: 5
Mean commits per author: 179.2
Development Distribution Score: 0.177
More commit stats: https://commits.ecosyste.ms/hosts/GitHub/repositories/parashardhapola/scarf
Topics: big-data, bioinformatics, cite-seq, clustering, differential-expression, dimension-reduction, gene-modules, genomics, graph-analytics, memory-efficient, multiomics, pseudotime, scalable-data-analysis, scatac-seq, scrna-seq, single-cell-atac-seq, single-cell-genomics, single-cell-rna-seq, tsne, umap
Files
Dependencies
- ipython-autotime >=0.3.1
- ipywidgets *
- jedi >=0.17.0
- jinja2 *
- myst-nb >=0.12.3
- myst-parser >=0.13.7
- nbclient <0.6
- sphinx >=3.5.4
- sphinx-book-theme >=0.0.35
- sphinx-copybutton >=0.2.12
- sphinx-external-toc >=0.2.1
- sphinx-tabs >=0.3.1
- sphinx_autodoc_typehints >=1.10.1
- topacedo >=0.2.6
- cmocean *
- dask >=2021.8.1
- datashader *
- gensim *
- h5py >=3.3.0
- hnswlib *
- importlib_metadata *
- joblib *
- kneed *
- leidenalg *
- loguru *
- matplotlib *
- networkx *
- numba *
- numcodecs *
- numpy *
- packaging *
- pandas *
- requests *
- scikit-learn *
- scikit-network ==0.24.0
- scipy *
- seaborn *
- setuptools *
- sparse *
- statsmodels *
- threadpoolctl *
- tqdm *
- umap-learn *
- zarr *
- actions/checkout v2 composite
- actions/setup-python v2 composite
- pypa/gh-action-pypi-publish 27b31702a0e7fc50959f5ad993c78deac1bdfc29 composite
- actions/checkout v2 composite
- actions/setup-python v2 composite
- codecov/codecov-action v3 composite
- ubuntu 20.04 build