HelloWorldLTY

Questions about problems in ingest related to pynndescent

12

Sorry to disturb, but it seems that the ingest method in scanpy meets some problems caused by pynndescent and numba. Here are the details: KeyError Traceback (most recent call last)...

Questions about sc.pp.scale and sc.tl.pca

4

Hi, I found that in some tutorial documents, they does not use sc.pp.scale before sc.tl.pca. https://scanpy-tutorials.readthedocs.io/en/latest/integrating-data-using-ingest.html But for some documents, they used. https://scanpy-tutorials.readthedocs.io/en/latest/pbmc3k.html This thing also happened in several tools'...

Could I directly use all the gene as input data for harmony model without feature selection? I think based on the tutorial it is ok. Thanks.

Squidpy cannot fit matplotlib 3.5.2

1

If I use matplotlib 3.5.2, I will receive this bug: [Matplotlib AttributeError: module 'matplotlib.cbook' has no attribute '_define_aliases'](https://stackoverflow.com/questions/53421905/matplotlib-attributeerror-module-matplotlib-cbook-has-no-attribute-define-a) If I use 3.5.0, the package can work normally. How to address...

Hi, I am trying to rewrite the process for getting the q value based on Pytorch, but I found that if I intend to use for loops, the running time...

Questions about figure size adjustment

1

Hi, I wonder if there are any methods I can use to adjust the figure size of the output figure of Seurat, for example, Vlnplot() Can I use something like...

Have trouble on installing the package

3

warnings.warn(ABI_INCOMPATIBILITY_WARNING.format(compiler)) building 'torch_geometric_autoscale._async' extension creating build/temp.linux-x86_64-cpython-38 creating build/temp.linux-x86_64-cpython-38/csrc gcc -pthread -B /gpfs/gibbs/pi/zhao/tl688/conda_envs/graphnn/compiler_compat -Wl,--sysroot=/ -Wsign-compare -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -fPIC -Icsrc -I/home/tl688/.local/lib/python3.8/site-packages/torch/include -I/home/tl688/.local/lib/python3.8/site-packages/torch/include/torch/csrc/api/include -I/home/tl688/.local/lib/python3.8/site-packages/torch/include/TH -I/home/tl688/.local/lib/python3.8/site-packages/torch/include/THC -I/gpfs/gibbs/pi/zhao/tl688/conda_envs/graphnn/include/python3.8 -c csrc/async.cpp -o...

/lib64/libc.so.6: version `GLIBC_2.25' not found

4

I meet this error when I intend to run GSEA on my python. Could you please suggest me some solutions? Thanks a lot.

Hi, I check your pre-training codes and I found that you used a 5-layer GNN with embedding space=300. I think it is not a very large model and I wonder...

https://github.com/stuart-lab/signac/issues/1256 Hi, could you please take a look at this issue? I use saveRDS and load data, it works well, but for saveh5seurat, it failed.