requirements.txt

absl-py==1.4.0
adjustText==0.8
aiofiles==22.1.0
aiohttp==3.8.4
aiosignal==1.3.1
aiosqlite==0.19.0
anndata==0.9.1
anyio==3.7.0
argon2-cffi==21.3.0
argon2-cffi-bindings==21.2.0
arrow==1.2.3
asttokens==2.2.1
astunparse==1.6.3
async-timeout==4.0.2
attrs==23.1.0
backcall==0.2.0
beautifulsoup4==4.12.2
bleach==6.0.0
blessed==1.20.0
blosc2==2.0.0
brokenaxes==0.5.0
cached-property==1.5.2
cachetools==5.3.1
cattrs==23.1.2
cellrank==2.0.1
certifi==2023.5.7
cffi==1.15.1
charset-normalizer==3.1.0
chex==0.1.7
click==8.1.3
cloudpickle==2.2.1
cmake==3.26.4
comm==0.1.3
contextlib2==21.6.0
contourpy==1.1.0
croniter==1.3.15
cycler==0.11.0
Cython @ file:///opt/conda/conda-bld/cython_1663692770955/work
dateutils==0.6.12
debugpy==1.6.7
decorator==5.1.1
deepdiff==6.3.0
defusedxml==0.7.1
Deprecated==1.2.14
dm-tree==0.1.8
docrep==0.3.2
elpigraph-python==0.2.7
equinox==0.11.1
et-xmlfile==1.1.0
etils==1.3.0
exceptiongroup==1.1.1
executing==1.2.0
fa2 @ file:///maps/projects/dan1/data/Brickman/projects/proks-salehin-et-al-2023/forceatlas2
fastapi==0.98.0
fastjsonschema==2.17.1
fcsparser==0.2.6
filelock==3.12.2
flatbuffers==23.5.26
flax==0.6.11
fonttools==4.40.0
fqdn==1.5.1
frozenlist==1.3.3
fsspec==2023.6.0
future==0.18.3
gast==0.4.0
google-auth==2.21.0
google-auth-oauthlib==1.0.0
google-pasta==0.2.0
gprofiler-official==1.0.0
graphtools==1.5.3
graphviz==0.20.1
grpcio==1.51.3
gtftools==0.9.0
h11==0.14.0
h5py==3.9.0
huggingface-hub==0.20.3
hyperopt==0.2.7
idna==3.4
igraph==0.10.4
importlib-resources==5.12.0
inquirer==3.1.3
ipykernel==6.23.2
ipython==8.14.0
ipywidgets==8.1.1
isoduration==20.11.0
itsdangerous==2.1.2
jax==0.4.13
jaxlib==0.4.13+cuda11.cudnn86
jaxopt==0.8.1
jaxtyping==0.2.23
jedi==0.18.2
Jinja2==3.0.3
joblib==1.2.0
jsonpointer==2.4
jsonschema==4.17.3
jupyter-events==0.6.3
jupyter-ydoc==1.0.2
jupyter_client==8.2.0
jupyter_collaboration==1.0.0
jupyter_core==5.3.1
jupyter_server==2.6.0
jupyter_server_fileid==0.9.0
jupyter_server_terminals==0.4.4
jupyterlab-pygments==0.2.2
jupyterlab-widgets==3.0.9
keras==2.12.0
kiwisolver==1.4.4
leidenalg==0.9.1
libclang==16.0.0
lightning==2.0.4
lightning-cloud==0.5.37
lightning-utilities==0.8.0
lineax==0.0.3
lit==16.0.6
llvmlite==0.40.1
loompy==3.0.7
Markdown==3.4.3
markdown-it-py==3.0.0
MarkupSafe==2.1.3
matplotlib==3.7.1
matplotlib-inline==0.1.6
matplotlib-venn==0.11.9
mdurl==0.1.2
mistune==3.0.1
ml-collections==0.1.1
ml-dtypes==0.2.0
mlxtend==0.23.0
moscot==0.3.3
mpmath==1.3.0
msgpack==1.0.5
mudata==0.2.3
multidict==6.0.4
multipledispatch==0.6.0
natsort==8.4.0
nbclient==0.8.0
nbconvert==7.6.0
nbformat==5.9.0
nest-asyncio==1.5.6
networkx==2.8.8
numba==0.57.1
numexpr==2.8.4
numpy==1.23.5
numpy-groupies==0.9.22
numpyro==0.12.1
nvidia-cublas-cu11==11.10.3.66
nvidia-cuda-cupti-cu11==11.7.101
nvidia-cuda-nvrtc-cu11==11.7.99
nvidia-cuda-runtime-cu11==11.7.99
nvidia-cudnn-cu11==8.6.0.163
nvidia-cufft-cu11==10.9.0.58
nvidia-curand-cu11==10.2.10.91
nvidia-cusolver-cu11==11.4.0.1
nvidia-cusparse-cu11==11.7.4.91
nvidia-nccl-cu11==2.14.3
nvidia-nvtx-cu11==11.7.91
oauthlib==3.2.2
openpyxl==3.1.2
opt-einsum==3.3.0
optax==0.1.5
orbax-checkpoint==0.2.6
ordered-set==4.1.0
ott-jax==0.4.4
overrides==7.3.1
packaging==23.1
palantir==1.2
pandas==1.5.3
pandocfilters==1.5.0
parso==0.8.3
patsy==0.5.3
pexpect==4.8.0
phate==1.0.11
PhenoGraph==1.5.7
pickleshare==0.7.5
Pillow==9.5.0
platformdirs==3.8.0
plotly==5.15.0
plottable==0.1.5
progressbar2==4.2.0
prometheus-client==0.17.0
prompt-toolkit==3.0.38
protobuf==4.23.3
psutil==5.9.5
ptyprocess==0.7.0
pure-eval==0.2.2
py-cpuinfo==9.0.0
py4j==0.10.9.7
pyaml==23.9.7
pyarrow==12.0.1
pyasn1==0.5.0
pyasn1-modules==0.3.0
pybiomart==0.2.0
pycparser==2.21
pydantic==1.10.9
pygam==0.9.0
Pygments==2.15.1
pygpcca==1.0.4
PyGSP==0.5.1
PyJWT==2.7.0
pymde==0.1.18
pynndescent==0.5.10
pyparsing==3.1.0
pyro-api==0.1.2
pyro-ppl==1.8.5
pyrsistent==0.19.3
python-dateutil==2.8.2
python-editor==1.0.4
python-igraph==0.10.4
python-json-logger==2.0.7
python-multipart==0.0.6
python-utils==3.7.0
pytorch-lightning==2.0.4
pytz==2023.3
PyYAML==6.0
pyzmq==25.1.0
ray==2.5.1
readchar==4.0.5
requests==2.31.0
requests-cache==1.1.0
requests-oauthlib==1.3.1
rfc3339-validator==0.1.4
rfc3986-validator==0.1.1
rich==13.6.0
rsa==4.9
s-gd2==1.8.1
scanpy==1.9.3
scFates==1.0.2
scgen @ git+https://github.com/theislab/scgen.git@06084773e56cad0dec340138441dee47a39af752
scib-metrics==0.3.3
SciencePlots==2.1.1
scikit-learn==1.2.2
scikit-misc==0.2.0
scikit-optimize==0.9.0
scipy==1.10.1
scprep==1.2.3
scvelo==0.2.5
scvi-tools==1.0.0
seaborn==0.11.2
Send2Trash==1.8.2
session-info==1.0.0
shap @ file:///maps/projects/dan1/data/Brickman/projects/proks-salehin-et-al-2023/scripts/third-party/shap
shapely==2.0.1
simpleppt==1.1.3
six==1.16.0
slicer==0.0.7
sniffio==1.3.0
soupsieve==2.4.1
sparse==0.14.0
squarify==0.4.3
stack-data==0.6.2
starlette==0.27.0
starsessions==1.3.0
statannotations==0.5.0
statsmodels==0.14.0
stdlib-list==0.9.0
sympy==1.12
tables==3.8.0
tasklogger==1.2.0
tenacity==8.2.2
tensorboard==2.12.3
tensorboard-data-server==0.7.1
tensorboardX==2.6.1
tensorflow==2.12.0
tensorflow-estimator==2.12.0
tensorflow-io-gcs-filesystem==0.32.0
tensorstore==0.1.39
termcolor==2.3.0
terminado==0.17.1
texttable==1.6.7
threadpoolctl==3.1.0
tinycss2==1.2.1
toolz==0.12.0
torch==2.0.1
torchmetrics==0.11.4
torchvision==0.15.2
tornado==6.3.2
tqdm==4.65.0
traitlets==5.9.0
triton==2.0.0
typeguard==2.13.3
typing_extensions==4.6.3
tzdata==2023.3
tzlocal==5.0.1
umap-learn==0.5.3
UpSetPlot==0.8.0
uri-template==1.3.0
url-normalize==1.4.3
urllib3==1.26.16
uvicorn==0.22.0
wcwidth==0.2.6
webcolors==1.13
webencodings==0.5.1
websocket-client==1.6.0
websockets==11.0.3
Werkzeug==2.3.6
widgetsnbextension==4.0.9
wrapt==1.14.1
xarray==2023.5.0
xgboost==1.7.6
XlsxWriter==3.1.9
y-py==0.6.0
yarl==1.9.2
ypy-websocket==0.8.4