requirements.txt

absl-py==2.0.0
adjustText==0.8
aiobotocore==2.5.4
aiohttp==3.8.6
aioitertools==0.11.0
aiosignal==1.3.1
airr==1.5.0
alabaster==0.7.13
alembic==1.13.1
altair==5.1.2
anndata==0.10.3
annotated-types==0.6.0
annoy==1.17.3
ansicon==1.89.0
anyio==3.7.1
appdirs==1.4.4
array-api-compat==1.4
arrow==1.3.0
asciitree==0.3.3
asttokens==2.4.0
astunparse==1.6.3
async-timeout==4.0.3
attrs==23.2.0
autoflake==2.3.1
awkward==2.6.3
awkward-cpp==32
Babel==2.13.1
backcall==0.2.0
backoff==2.2.1
bcbio-gff==0.7.0
beautifulsoup4==4.12.2
binaryornot==0.4.4
biopython==1.81
bleach==6.1.0
blessed==1.20.0
blinker==1.6.3
bokeh==3.3.0
boto3==1.28.72
botocore==1.31.17
bottle==0.12.25
build==1.0.3
cachetools==5.3.1
cachey==0.2.1
captum==0.7.0
catboost==1.2.3
cell2location==0.1.3
celltypist==1.6.2
certifi==2023.7.22
cffi==1.16.0
cfgv==3.4.0
chardet==5.2.0
charset-normalizer==3.3.0
chex==0.1.7
click==8.1.7
click-plugins==1.1.1
cligj==0.7.2
cloudpickle==3.0.0
colorama==0.4.6
colorcet==3.0.1
colorlog==6.8.2
comet-ml==3.35.5
comm==0.1.4
ConfigArgParse==1.7
configobj==5.0.8
connection-pool==0.0.3
contextlib2==21.6.0
contourpy==1.1.1
cookiecutter==2.4.0
croniter==1.4.1
curl_cffi==0.6.2
cycler==0.12.1
Cython==3.0.7
dacite==1.8.1
dask==2023.10.0
dask-image==2023.8.1
dataclasses==0.6
dataclasses-json==0.5.14
datashader==0.16.0
dateutils==0.6.12
datrie==0.8.2
debugpy==1.8.0
decorator==4.4.2
deepdiff==6.6.1
deeplake==3.8.22
dill==0.3.8
diskcache==5.6.3
distlib==0.3.7
distributed==2023.10.0
distro==1.9.0
dm-tree==0.1.8
docker==7.0.0
docopt==0.6.2
docrep==0.3.2
docstring-parser==0.15
docutils==0.20.1
dpath==2.1.6
duckduckgo_search==4.5.0
dulwich==0.21.7
edgepy==0.1.33.dev0
et-xmlfile==1.1.0
etils==1.5.2
everett==3.1.0
exceptiongroup==1.1.3
executing==2.0.0
ezpip==0.2.5
fastapi==0.104.0
fasteners==0.19
fastjsonschema==2.18.1
fbpca==1.0
fies==1.4.0
fileinit==0.0.2
filelock==3.12.4
fiona==1.9.5
flatbuffers==23.5.26
flax==0.7.4
fonttools==4.43.1
freetype-py==2.4.0
frozenlist==1.4.0
fsspec==2023.6.0
gast==0.4.0
gdown==5.1.0
geopandas==0.14.0
geosketch==1.2
gitdb==4.0.10
GitPython==3.1.37
google-auth==2.23.3
google-auth-oauthlib==0.4.6
google-pasta==0.2.0
GraphST==1.1.1
graphviz==0.20.1
greenlet==3.0.3
grpcio==1.59.0
gseapy==1.0.6
h11==0.14.0
h5py==3.10.0
HeapDict==1.0.1
hilearn==0.2.2
holoviews==1.18.3
hotspotsc @ git+https://github.com/yoseflab/Hotspot.git@42ce35c5be336aba19c8fdc97294feb99f6db8b9
hsluv==5.0.4
htmlmin==0.1.12
httpcore==1.0.4
httpx==0.27.0
huggingface-hub==0.21.4
humanfriendly==10.0
humbug==0.3.2
identify==2.5.33
idna==3.4
igraph==0.10.8
ImageHash==4.3.1
imageio==2.31.6
imagesize==1.4.1
importlib-metadata==6.8.0
importlib-resources==6.1.0
inflect==7.0.0
inquirer==3.1.3
intervaltree==3.1.0
ipykernel==6.26.0
ipython==8.16.1
ipython-genutils==0.2.0
ipywidgets==8.1.1
isort==5.13.2
itsdangerous==2.1.2
jax==0.4.19
jaxlib==0.4.19
jedi==0.19.1
Jinja2==3.1.2
jinxed==1.2.0
jmespath==1.0.1
joblib==1.3.2
json-stock==0.2.6
jsonpatch==1.33
jsonpointer==2.4
jsonschema==4.19.1
jsonschema-specifications==2023.7.1
jupyter_client==8.5.0
jupyter_core==5.4.0
jupyterlab-widgets==3.0.9
keras==2.11.0
kiwisolver==1.4.5
langchain==0.0.208
langchain-community==0.0.25
langchain-core==0.1.29
langchain-text-splitters==0.0.1
langchainplus-sdk==0.0.20
langsmith==0.1.20
lazy_loader==0.3
legacy-api-wrap==1.4
leidenalg==0.10.1
lets-plot==4.0.1
Levenshtein==0.25.1
libclang==16.0.6
libpysal==4.9.2
lightgbm==4.3.0
lightning==2.0.9.post0
lightning-cloud==0.5.44
lightning-utilities==0.9.0
linkify-it-py==2.0.3
llvmlite==0.41.0
locket==1.0.0
loguru==0.7.2
looseversion==1.3.0
louvain==0.8.1
lxml==5.1.0
lz4==4.3.3
magicgui==0.8.0
Mako==1.3.2
Markdown==3.5
markdown-it-py==3.0.0
MarkupSafe==2.1.3
marshmallow==3.21.1
matplotlib==3.8.0
matplotlib-inline==0.1.6
matplotlib-scalebar==0.8.1
matplotlib-venn==0.11.10
mdit-py-plugins==0.4.0
mdurl==0.1.2
mizani==0.9.3
ml-collections==0.1.1
ml-dtypes==0.3.1
mpmath==1.3.0
msgpack==1.0.7
mudata==0.2.3
mult==1.1.1
multidict==6.0.4
multimethod==1.11
multipledispatch==1.0.0
multiprocess==0.70.16
multiscale_spatial_image==0.11.2
muon==0.1.5
mvtcr==0.2.0
mypy-extensions==1.0.0
NaiveDE==1.2.0
napari==0.4.15
napari-console==0.0.9
napari-plugin-engine==0.2.0
napari-svg==0.1.10
natsort==8.4.0
nbformat==5.9.2
nest-asyncio==1.5.8
networkx==3.1
newick==1.0.0
nodeenv==1.8.0
npe2==0.7.3
numba==0.58.0
numcodecs==0.12.1
numexpr==2.9.0
numpy==1.23.4
numpydoc==1.6.0
numpyro==0.13.2
oauthlib==3.2.2
ome-zarr==0.8.2
omnipath==1.0.7
openai==0.27.8
openapi-schema-pydantic==1.2.4
opencv-python==4.8.1.78
openpyxl==3.1.2
opt-einsum==3.3.0
optax==0.1.7
optuna==3.4.0
optuna-dashboard==0.14.0
orbax-checkpoint==0.4.1
ordered-set==4.1.0
orjson==3.9.15
outcome==1.3.0.post0
packaging==23.2
palettable==3.3.3
pandas==2.2.2
pandas-profiling==3.6.6
panel==1.3.8
param==2.0.0
parasail==1.3.4
parso==0.8.3
partd==1.4.1
pathos==0.3.2
patsy==0.5.3
phik==0.12.4
pickleshare==0.7.5
Pillow==10.0.1
PIMS==0.6.1
pinecone-client==3.1.0
Pint==0.22
pipreqs==0.4.13
plac==1.4.0
platformdirs==3.11.0
plotly==5.17.0
plotnine==0.12.3
polars==0.20.19
pooch==1.8.1
POT==0.9.3
pox==0.3.4
ppft==1.7.6.8
pre-commit==3.5.0
prompt-toolkit==3.0.39
protobuf==3.19.6
psutil==5.9.6
psygnal==0.9.4
PuLP==2.7.0
pure-eval==0.2.2
pyarrow==13.0.0
pyasn1==0.5.0
pyasn1-modules==0.3.0
pycairo==1.26.0
pyconify==0.1.6
pycparser==2.21
pyct==0.5.0
pydantic==2.1.1
pydantic_core==2.4.0
pydeck==0.8.1b0
pydeseq2==0.4.1
pyflakes==3.2.0
pygeos==0.14
Pygments==2.16.1
PyJWT==2.8.0
pynndescent==0.5.10
PyOpenGL==3.1.7
pyparsing==3.1.1
PyPDF2==3.0.1
pypng==0.20220715.0
pyproj==3.6.1
pyproject_hooks==1.0.0
PyQt5==5.15.10
PyQt5-Qt5==5.15.2
PyQt5-sip==12.13.0
pyreadline3==3.4.1
pyro-api==0.1.2
pyro-ppl==1.8.6
PySocks==1.7.1
python-box==6.1.0
python-dateutil==2.8.2
python-dotenv==1.0.1
python-editor==1.0.4
python-Levenshtein==0.25.1
python-multipart==0.0.6
python-slugify==8.0.1
pytorch-lightning==2.1.0
pytz==2023.3.post1
pyviz_comms==3.0.1
PyWavelets==1.4.1
pywin32==306
PyYAML==6.0.1
pyzmq==25.1.1
qtconsole==5.4.4
QtPy==2.4.1
rapidfuzz==3.8.1
read-roi==1.6.0
readchar==4.0.5
referencing==0.30.2
regex==2023.12.25
regional==1.1.2
relpath==3.0.5
rename-lock==0.1.4
requests==2.31.0
requests-oauthlib==1.3.1
requests-toolbelt==1.0.0
reretry==0.11.8
rich==13.6.0
rpds-py==0.10.6
rsa==4.9
s3fs==2023.6.0
s3transfer==0.7.0
sacremoses==0.1.1
safetensors==0.4.2
sanbomics==0.1.0
scanorama==1.7.4
scanpy==1.9.6
scArches==0.5.10
scHPL==1.0.5
scikit-image==0.20.0
scikit-learn==1.3.2
scikit-misc==0.3.1
scipy==1.11.3
scirpy==0.13.1
scrublet==0.2.3
scvi-tools==1.0.4
seaborn==0.13.2
seagal==2.5.2
selenium==4.18.1
semantic-version==2.10.0
sentry-sdk==1.45.0
seqtk==0.5.0
session-info==1.0.0
shap==0.44.1
shapely==2.0.2
showit==1.1.4
simplejson==3.19.2
six==1.16.0
slicedimage==4.1.1
slicer==0.0.7
slicerator==1.1.0
smart-open==6.4.0
smmap==5.0.1
snakemake==7.32.3
sniffio==1.3.0
snowballstemmer==2.2.0
sortedcontainers==2.4.0
soupsieve==2.5
sout==1.2.1
sparse==0.14.0
spatial_image==0.3.0
spatialdata==0.0.15
SpatialDE==1.1.3
SpatialDM==0.1.0
Sphinx==7.2.6
sphinxcontrib-applehelp==1.0.7
sphinxcontrib-devhelp==1.0.5
sphinxcontrib-htmlhelp==2.0.4
sphinxcontrib-jsmath==1.0.1
sphinxcontrib-qthelp==1.0.6
sphinxcontrib-serializinghtml==1.1.9
SQLAlchemy==2.0.27
squarify==0.4.3
squidpy==1.4.1
stack-data==0.6.3
starfish==0.2.2
starlette==0.27.0
starsessions==1.3.0
statsmodels==0.13.2
stdlib-list==0.9.0
stlearn==0.4.12
stopit==1.1.2
streamlit==1.31.1
streamlit-ace==0.1.1
streamlit-pandas-profiling==0.1.3
superqt==0.6.1
sympy==1.5.1
tabulate==0.9.0
tangled-up-in-unicode==0.2.0
tangram==0.7.0
tblib==3.0.0
tenacity==8.2.3
tensorboard==2.11.2
tensorboard-data-server==0.6.1
tensorboard-plugin-wit==1.8.1
tensorflow==2.11.1
tensorflow-estimator==2.11.0
tensorflow-intel==2.11.1
tensorflow-io-gcs-filesystem==0.31.0
tensorstore==0.1.46
termcolor==2.3.0
text-unidecode==1.3
texttable==1.7.0
threadpoolctl==3.2.0
throttler==1.2.2
tifffile==2023.9.26
tiktoken==0.6.0
tokenizers==0.15.2
toml==0.10.2
tomli==2.0.1
tomli_w==1.0.0
toolz==0.12.0
toposort==1.10
torch==2.1.0
torch-tb-profiler==0.4.3
torch_geometric==2.5.2
torchmetrics==1.2.0
tornado==6.3.3
tqdm==4.66.1
trackpy==0.6.1
traitlets==5.11.2
transformers==4.38.2
trio==0.25.0
trio-websocket==0.11.1
typeguard==4.1.5
typer==0.9.0
types-python-dateutil==2.8.19.14
typing-inspect==0.9.0
typing_extensions==4.10.0
tzdata==2023.3
tzlocal==5.1
uc-micro-py==1.0.3
umap-learn==0.5.4
urllib3==1.26.18
uvicorn==0.23.2
validators==0.22.0
virtualenv==20.25.0
visions==0.7.5
vispy==0.14.1
watchdog==3.0.0
wcwidth==0.2.8
webencodings==0.5.1
websocket-client==1.3.3
websockets==12.0
Werkzeug==3.0.1
widgetsnbextension==4.0.9
wikipedia==1.4.0
win32-setctime==1.1.0
wordcloud==1.9.3
wrapt==1.15.0
wsproto==1.2.0
wurlitzer==3.0.3
xarray==2023.10.1
xarray-dataclasses==1.7.0
xarray-datatree==0.0.12
xarray-schema==0.0.3
xarray-spatial==0.3.7
xgboost==2.0.3
xyzservices==2023.10.1
yamlordereddictloader==0.4.2
yarg==0.1.9
yarl==1.9.2
ydata-profiling==4.6.4
yte==1.5.1
zarr==2.16.1
zict==3.0.0
zipp==3.17.0