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Dependencies
- anndata >=0.8
- apybiomart
- beartype >=0.18.2
- boto3
- deprecation
- ipympl >=0.8.2
- ipython
- ipywidgets >=8.0.0
- jinja2
- kneed
- matplotlib >=3.8.4
- matplotlib-venn >=1.1.2
- numba >=0.57.1
- numpy >=2
- packaging
- pandas >1.5.3
- plotly
- pptreport >=1.1.4
- psutil
- pygithub
- pysam
- python-gitlab
- pyyaml
- qnorm
- requests >=2.32.5
- scanpy >=1.11
- scikit-image
- scipy >=1.14
- scrublet
- seaborn >0.12
- statsmodels >=0.14.5
- throttler
- tqdm
- upsetplot
31 optional dependencies
- adjusttext[pseudotime]
- anndata2ri[converter]
- bbknn[batch-correction]
- click[interactive]
- gseapy[gsea]
- harmonypy[batch-correction]
- liana[receptor-ligand]
- markerrepo[annotation]
- mofapy2[multiome]
- muon[multiome]
- networkx[receptor-ligand]
- palantir[pilot]
- palantir[palantir]
- peakqc[atac]
- plotnine[receptor-ligand]
- pybedtools[atac]
- pycirclize[receptor-ligand]
- pydeseq2[deseq2]
- pygenometracks[atac]
- pyranges[atac]
- rpy2[converter]
- sc-framework[core]
- sc-framework[downstream]
- sc-framework[all]
- scanorama[batch-correction]
- scanpro[proportion]
- scfates[pseudotime]
- scvelo[velocity]
- scvi-tools[batch-correction]
- tobias[atac]
- uropa[atac]