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Dependencies
- anndata >=0.8
- apybiomart
- beartype >=0.18.2
- boto3
- deprecation
- ipympl
- ipython
- ipywidgets >=8.0.0
- jinja2
- kneed
- matplotlib
- matplotlib-venn
- numba >=0.57.0rc1
- numpy >=2
- openpyxl
- packaging
- pandas >1.5.3
- plotly
- pptreport >=1.1.4
- psutil
- pysam
- python-gitlab
- pyyaml
- qnorm
- requests
- scanpy >=1.11
- scipy >=1.14
- scrublet
- seaborn >0.12
- statsmodels >=0.14.5
- throttler
- tqdm
- upsetplot
58 optional dependencies
- anndata2ri[converter]
- anndata2ri[all]
- anndata2ri[core]
- bbknn[core]
- bbknn[all]
- bbknn[batch-correction]
- click[interactive]
- click[all]
- click[core]
- gseapy[all]
- gseapy[downstream]
- gseapy[gsea]
- harmonypy[batch-correction]
- harmonypy[core]
- harmonypy[all]
- igraph[downstream]
- igraph[receptor-ligand]
- igraph[all]
- liana[all]
- liana[downstream]
- liana[receptor-ligand]
- mudata[receptor-ligand]
- mudata[all]
- mudata[downstream]
- networkx[downstream]
- networkx[all]
- networkx[receptor-ligand]
- peakqc[atac]
- peakqc[all]
- peakqc[core]
- pybedtools[core]
- pybedtools[all]
- pybedtools[atac]
- pycirclize[all]
- pycirclize[receptor-ligand]
- pycirclize[downstream]
- pydeseq2[downstream]
- pydeseq2[all]
- pydeseq2[deseq2]
- pygenometracks[atac]
- pygenometracks[core]
- pygenometracks[all]
- rpy2[converter]
- rpy2[all]
- rpy2[core]
- scanorama[batch-correction]
- scanorama[all]
- scanorama[core]
- scfates[pseudotime]
- scikit-learn[receptor-ligand]
- scikit-learn[all]
- scikit-learn[downstream]
- tobias[core]
- tobias[atac]
- tobias[all]
- uropa[all]
- uropa[atac]
- uropa[core]