pysam
matplotlib>=3.8.4
matplotlib_venn>=1.1.2
scanpy[leiden]>=1.11
anndata>=0.8
numba>=0.57.1
numpy>=2
kneed
qnorm
plotly
scipy>=1.14
statsmodels>=0.14.5
tqdm
pandas>1.5.3
seaborn>0.12
ipywidgets>=8.0.0
scrublet
IPython
ipympl>=0.8.2
apybiomart
requests>=2.32.5
python-gitlab
psutil
deprecation
pyyaml
beartype>=0.18.2
packaging
throttler
upsetplot
pptreport>=1.1.4
boto3
Jinja2
scikit-image
PyGithub

[all]
SC-Framework[core,downstream]

[annotation]
markerRepo>=0.1.5

[atac]
uropa
pybedtools>=0.9.1
pygenometracks>=3.9
peakqc
tobias>=0.17.2
pyranges

[batch_correction]
bbknn
harmonypy<=0.0.10
scanorama
scvi-tools

[converter]
rpy2
anndata2ri

[core]
SC-Framework[atac,batch_correction,converter,interactive]

[deseq2]
pydeseq2>=0.5.2

[downstream]
SC-Framework[annotation,deseq2,gsea,multiome,palantir,pilot,proportion,pseudotime,receptor_ligand,velocity]

[gsea]
gseapy>=1.2.1

[interactive]
click

[multiome]
muon>=0.1.7
mofapy2

[palantir]
palantir>=1.4.4

[pilot]
palantir>=1.4.4

[proportion]
scanpro>=0.4.1

[pseudotime]
scFates>=1.2.4
adjustText>=1.3.0

[receptor_ligand]
pycirclize>=1.10.1
liana>=1.7.0
networkx>=3.5
plotnine>=0.15.2

[velocity]
scvelo>=0.3.4
