Open CDchenlin opened 1 month ago
chanwkimlab
commented
1 month ago 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.
CDchenlin
commented
1 month ago 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
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