MONET
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suinleelab
Request for ’data‘ folder
Hello,
I wanted to express my gratitude for the outstanding work you’ve done! I must apologize if I’ve missed it, but I was unable to locate the ‘data’ folder in this repository, which is supposed to contain the ‘/pubmed/search_query.csv’ file and ‘/textbook/pdf_files’. Could you kindly let me know if there are any plans to release these pertinent resources?
Best Regards, Chenlin
Hi, thanks for your interest in our work! We've updated the repo to include the pubmed/search_query.csv file. As for other data, since they are raw data, we do not have plans to redistribute them.
Dear @chanwkimlab,
I greatly appreciate your response and nice work. It has been immensely helpful. However, I encountered an issue when executing scripts/preprocess/preprocess_pubmed.sh. The error message displayed is ModuleNotFoundError: No module named 'MONET'.
To the best of my knowledge, I have installed all necessary packages following the instructions in the Read Me file. I also attempted to resolve the issue by running pip install MONET, but the error remains.
For your reference, I have attached the package information from my Anaconda environment. I would be grateful if you could review it and let me know if I have missed anything.
_libgcc_mutex 0.1 conda_forge conda-forge
_openmp_mutex 4.5 2_gnu conda-forge
anndata 0.10.7 pypi_0 pypi
anyio 4.3.0 pypi_0 pypi
argon2-cffi 23.1.0 pypi_0 pypi
argon2-cffi-bindings 21.2.0 pypi_0 pypi
array-api-compat 1.6 pypi_0 pypi
arrow 1.3.0 pypi_0 pypi
asttokens 2.4.1 pypi_0 pypi
async-lru 2.0.4 pypi_0 pypi
attrs 23.2.0 pypi_0 pypi
babel 2.15.0 pypi_0 pypi
beautifulsoup4 4.12.3 pypi_0 pypi
bleach 6.1.0 pypi_0 pypi
bzip2 1.0.8 hd590300_5 conda-forge
ca-certificates 2024.2.2 hbcca054_0 conda-forge
certifi 2024.2.2 pypi_0 pypi
cffi 1.16.0 pypi_0 pypi
charset-normalizer 3.3.2 pypi_0 pypi
click 7.1.2 pypi_0 pypi
clip 1.0 pypi_0 pypi
comm 0.2.2 pypi_0 pypi
contourpy 1.2.1 pypi_0 pypi
cycler 0.12.1 pypi_0 pypi
cython 0.29.37 pypi_0 pypi
debugpy 1.8.1 pypi_0 pypi
decorator 5.1.1 pypi_0 pypi
defusedxml 0.7.1 pypi_0 pypi
exceptiongroup 1.2.1 pypi_0 pypi
executing 2.0.1 pypi_0 pypi
fastjsonschema 2.19.1 pypi_0 pypi
filelock 3.14.0 pypi_0 pypi
fonttools 4.51.0 pypi_0 pypi
fqdn 1.5.1 pypi_0 pypi
fsspec 2024.3.1 pypi_0 pypi
ftfy 6.2.0 pypi_0 pypi
get-annotations 0.1.2 pypi_0 pypi
h11 0.14.0 pypi_0 pypi
h5py 3.11.0 pypi_0 pypi
httpcore 1.0.5 pypi_0 pypi
httpx 0.27.0 pypi_0 pypi
huggingface-hub 0.22.0 pypi_0 pypi
idna 3.7 pypi_0 pypi
importlib-metadata 7.1.0 pypi_0 pypi
importlib-resources 6.4.0 pypi_0 pypi
ipykernel 6.29.4 pypi_0 pypi
ipython 8.18.1 pypi_0 pypi
ipywidgets 8.1.2 pypi_0 pypi
isoduration 20.11.0 pypi_0 pypi
jedi 0.19.1 pypi_0 pypi
jinja2 3.1.4 pypi_0 pypi
joblib 1.4.2 pypi_0 pypi
json5 0.9.25 pypi_0 pypi
jsonpointer 2.4 pypi_0 pypi
jsonschema 4.22.0 pypi_0 pypi
jsonschema-specifications 2023.12.1 pypi_0 pypi
jupyter 1.0.0 pypi_0 pypi
jupyter-client 8.6.1 pypi_0 pypi
jupyter-console 6.6.3 pypi_0 pypi
jupyter-core 5.7.2 pypi_0 pypi
jupyter-events 0.10.0 pypi_0 pypi
jupyter-lsp 2.2.5 pypi_0 pypi
jupyter-server 2.14.0 pypi_0 pypi
jupyter-server-terminals 0.5.3 pypi_0 pypi
jupyterlab 4.1.8 pypi_0 pypi
jupyterlab-pygments 0.3.0 pypi_0 pypi
jupyterlab-server 2.27.1 pypi_0 pypi
jupyterlab-widgets 3.0.10 pypi_0 pypi
kiwisolver 1.4.5 pypi_0 pypi
ld_impl_linux-64 2.40 h55db66e_0 conda-forge
legacy-api-wrap 1.4 pypi_0 pypi
libffi 3.4.2 h7f98852_5 conda-forge
libgcc-ng 13.2.0 h77fa898_7 conda-forge
libgomp 13.2.0 h77fa898_7 conda-forge
libnsl 2.0.1 hd590300_0 conda-forge
libsqlite 3.45.3 h2797004_0 conda-forge
libuuid 2.38.1 h0b41bf4_0 conda-forge
libzlib 1.2.13 hd590300_5 conda-forge
llvmlite 0.42.0 pypi_0 pypi
markupsafe 2.1.5 pypi_0 pypi
matplotlib 3.8.4 pypi_0 pypi
matplotlib-inline 0.1.7 pypi_0 pypi
mistune 3.0.2 pypi_0 pypi
monet 0.3.1 pypi_0 pypi
mpmath 1.3.0 pypi_0 pypi
natsort 8.4.0 pypi_0 pypi
nbclient 0.10.0 pypi_0 pypi
nbconvert 7.16.4 pypi_0 pypi
nbformat 5.10.4 pypi_0 pypi
ncurses 6.5 h59595ed_0 conda-forge
nest-asyncio 1.6.0 pypi_0 pypi
networkx 3.2.1 pypi_0 pypi
notebook 7.1.3 pypi_0 pypi
notebook-shim 0.2.4 pypi_0 pypi
numba 0.59.1 pypi_0 pypi
numpy 1.26.4 pypi_0 pypi
nvidia-cublas-cu12 12.1.3.1 pypi_0 pypi
nvidia-cuda-cupti-cu12 12.1.105 pypi_0 pypi
nvidia-cuda-nvrtc-cu12 12.1.105 pypi_0 pypi
nvidia-cuda-runtime-cu12 12.1.105 pypi_0 pypi
nvidia-cudnn-cu12 8.9.2.26 pypi_0 pypi
nvidia-cufft-cu12 11.0.2.54 pypi_0 pypi
nvidia-curand-cu12 10.3.2.106 pypi_0 pypi
nvidia-cusolver-cu12 11.4.5.107 pypi_0 pypi
nvidia-cusparse-cu12 12.1.0.106 pypi_0 pypi
nvidia-nccl-cu12 2.20.5 pypi_0 pypi
nvidia-nvjitlink-cu12 12.4.127 pypi_0 pypi
nvidia-nvtx-cu12 12.1.105 pypi_0 pypi
openssl 3.3.0 hd590300_0 conda-forge
overrides 7.7.0 pypi_0 pypi
packaging 24.0 pypi_0 pypi
pandas 2.2.2 pypi_0 pypi
pandocfilters 1.5.1 pypi_0 pypi
parso 0.8.4 pypi_0 pypi
patsy 0.5.6 pypi_0 pypi
pexpect 4.9.0 pypi_0 pypi
pillow 10.3.0 pypi_0 pypi
pip 24.0 pyhd8ed1ab_0 conda-forge
platformdirs 4.2.1 pypi_0 pypi
plotly 5.22.0 pypi_0 pypi
prometheus-client 0.20.0 pypi_0 pypi
prompt-toolkit 3.0.43 pypi_0 pypi
psutil 5.9.8 pypi_0 pypi
ptyprocess 0.7.0 pypi_0 pypi
pure-eval 0.2.2 pypi_0 pypi
pycparser 2.22 pypi_0 pypi
pygments 2.18.0 pypi_0 pypi
pynndescent 0.5.12 pypi_0 pypi
pyparsing 3.1.2 pypi_0 pypi
python 3.9.15 hba424b6_0_cpython conda-forge
python-dateutil 2.9.0.post0 pypi_0 pypi
python-json-logger 2.0.7 pypi_0 pypi
pytz 2024.1 pypi_0 pypi
pyyaml 6.0.1 pypi_0 pypi
pyzmq 26.0.3 pypi_0 pypi
qtconsole 5.5.2 pypi_0 pypi
qtpy 2.4.1 pypi_0 pypi
readline 8.2 h8228510_1 conda-forge
referencing 0.35.1 pypi_0 pypi
regex 2024.5.10 pypi_0 pypi
requests 2.31.0 pypi_0 pypi
rfc3339-validator 0.1.4 pypi_0 pypi
rfc3986-validator 0.1.1 pypi_0 pypi
rpds-py 0.18.1 pypi_0 pypi
safetensors 0.4.3 pypi_0 pypi
scanpy 1.10.1 pypi_0 pypi
scikit-learn 1.4.2 pypi_0 pypi
scipy 1.13.0 pypi_0 pypi
seaborn 0.13.2 pypi_0 pypi
send2trash 1.8.3 pypi_0 pypi
session-info 1.0.0 pypi_0 pypi
setuptools 69.5.1 pyhd8ed1ab_0 conda-forge
six 1.16.0 pypi_0 pypi
sniffio 1.3.1 pypi_0 pypi
soupsieve 2.5 pypi_0 pypi
stack-data 0.6.3 pypi_0 pypi
statsmodels 0.14.2 pypi_0 pypi
stdlib-list 0.10.0 pypi_0 pypi
sympy 1.12 pypi_0 pypi
tenacity 8.3.0 pypi_0 pypi
terminado 0.18.1 pypi_0 pypi
threadpoolctl 3.5.0 pypi_0 pypi
tinycss2 1.3.0 pypi_0 pypi
tk 8.6.13 noxft_h4845f30_101 conda-forge
tokenizers 0.15.2 pypi_0 pypi
tomli 2.0.1 pypi_0 pypi
torch 2.3.0 pypi_0 pypi
torchaudio 2.3.0 pypi_0 pypi
torchvision 0.18.0 pypi_0 pypi
tornado 6.4 pypi_0 pypi
tqdm 4.66.4 pypi_0 pypi
traitlets 5.14.3 pypi_0 pypi
transformers 4.39.1 pypi_0 pypi
triton 2.3.0 pypi_0 pypi
types-python-dateutil 2.9.0.20240316 pypi_0 pypi
typing-extensions 4.11.0 pypi_0 pypi
tzdata 2024.1 pypi_0 pypi
umap-learn 0.5.6 pypi_0 pypi
uri-template 1.3.0 pypi_0 pypi
urllib3 2.2.1 pypi_0 pypi
wcwidth 0.2.13 pypi_0 pypi
webcolors 1.13 pypi_0 pypi
webencodings 0.5.1 pypi_0 pypi
websocket-client 1.8.0 pypi_0 pypi
wheel 0.43.0 pyhd8ed1ab_1 conda-forge
widgetsnbextension 4.0.10 pypi_0 pypi
xlmhg 2.5.4 pypi_0 pypi
xz 5.2.6 h166bdaf_0 conda-forge
zipp 3.18.1 pypi_0 pypi
Thank you once again for your invaluable assistance!
Best Regards, Chenlin