System Requirements

DeepGFT can run on Linux and Windows. The package has been tested on the following systems:

• Linux: CentOS 7

• Windows: Windows 10

DeepGFT requires python version >= 3.7. We tested it in python 3.8.16 and cuda 11.6.1 on Linux. The following is our environment during testing：

anndata==0.8.0
backports.zoneinfo==0.2.1
biothings-client==0.3.0
certifi==2022.12.7
cffi==1.15.1
charset-normalizer==3.1.0
contourpy==1.0.7
cycler==0.11.0
fonttools==4.39.2
h5py==3.8.0
idna==3.4
igraph==0.10.4
importlib-metadata==6.1.0
importlib-resources==5.12.0
Jinja2==3.1.2
joblib==1.2.0
kiwisolver==1.4.4
kneed==0.8.2
llvmlite==0.39.1
louvain==0.8.0
MarkupSafe==2.1.2
matplotlib==3.7.1
mygene==3.2.2
natsort==8.3.1
networkx==3.0
numba==0.56.4
numpy==1.23.5
packaging==23.0
pandas==1.5.3
patsy==0.5.3
Pillow==9.4.0
POT==0.8.2
psutil==5.9.4
pycparser==2.21
pynndescent==0.5.8
pyparsing==3.0.9
python-dateutil==2.8.2
python-igraph==0.10.4
pytz==2022.7.1
pytz-deprecation-shim==0.1.0.post0
requests==2.28.2
rpy2==3.5.10
scanpy==1.9.3
scikit-learn==1.2.2
scipy==1.8.0
seaborn==0.12.2
session-info==1.0.0
six==1.16.0
statsmodels==0.13.5
stdlib-list==0.8.0
texttable==1.6.7
threadpoolctl==3.1.0
torch==1.12.0+cu116
torch-cluster @ file:///fs/ess/PAS1475/Jixin/DeepGFT_proj/torch_cluster-1.6.0%2Bpt112cu116-cp38-cp38-linux_x86_64.whl
torch-geometric==2.1.0
torch-scatter @ file:///fs/ess/PAS1475/Jixin/DeepGFT_proj/torch_scatter-2.1.0%2Bpt112cu116-cp38-cp38-linux_x86_64.whl
torch-sparse @ file:///fs/ess/PAS1475/Jixin/DeepGFT_proj/torch_sparse-0.6.16%2Bpt112cu116-cp38-cp38-linux_x86_64.whl
torchaudio==0.12.0+cu116
torchvision==0.13.0+cu116
tqdm==4.65.0
typing_extensions==4.5.0
tzdata==2022.7
tzlocal==4.3
umap-learn==0.5.3
urllib3==1.26.15
zipp==3.15.0