kchen-lab / scmer Goto Github PK

Hi,

Thank you so much for sharing this tool. I am not sure how to deal batch effect before running this pipeline? Thank you so much.

Best,

Zhen

Hi, I am trying to run the example in
https://htmlpreview.github.io/?https://github.com/KChen-lab/SCMER/blob/master/notebooks/melanoma-gpu-with-batch-in-r.nb.html

I wonder where I can get the input files.

'melanoma.txt.gz'
"genes.txt"
"melanoma_batches.txt"

Thank you!

I tried in several machines install scmer but I get this error:

ERROR: Failed cleaning build dir for numpy
      Failed to build numpy
      ERROR: Could not build wheels for numpy, which is required to install pyproject.toml-based projects
      [end of output]

  note: This error originates from a subprocess, and is likely not a problem with pip.
error: subprocess-exited-with-error

× pip subprocess to install build dependencies did not run successfully.
│ exit code: 1
╰─> See above for output.

note: This error originates from a subprocess, and is likely not a problem with pip.

I want to know which requirements we need, in the requirements file we have only the scikit-learn version, could you please provide the correct versions for torch, numpy, scipy, pandas, and seaborn?

Thanks a lot! 😄

Hi!
Running into next error while trying to install SCMER:

(base) C02ZC54JLVDL:Develop alsu$ git clone https://github.com/KChen-lab/SCMER.git
Cloning into 'SCMER'...
remote: Enumerating objects: 485, done.
fatal: the remote end hung up unexpectedlyiB | 2.90 MiB/s
fatal: early EOF
fatal: index-pack failed