ncem
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theislab
Learning cell communication from spatial graphs of cells
Bumps [actions/checkout](https://github.com/actions/checkout) from 2 to 3. Release notes Sourced from actions/checkout's releases. v3.0.0 Updated to the node16 runtime by default This requires a minimum Actions Runner version of v2.285.0 to...
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Bumps [actions/cache](https://github.com/actions/cache) from 2.1.6 to 3.3.1. Release notes Sourced from actions/cache's releases. v3.3.1 What's Changed Reduced download segment size to 128 MB and timeout to 10 minutes by @kotewar in...
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Bumps [pre-commit](https://github.com/pre-commit/pre-commit) from 2.12.0 to 2.21.0. Release notes Sourced from pre-commit's releases. pre-commit v2.21.0 Features Require new-enough virtualenv to prevent 3.10 breakage #2467 PR by @asottile. Respect aliases with SKIP...
**Describe the bug** Hello Author, I am following your tutorial https://github.com/theislab/ncem_tutorials/blob/main/tutorials/type_coupling_visium.ipynb In total, I have 3 slides 10x visium using the same preprocessing, There are 2 samples I've got error...
**Question** Dear @AnnaChristina and ncem developers, thank you for creating this impressive tool! I am studying immune signalling in the visium data. For this reason, I deconvoluted a single cell...
Hello ncem team, Thanks to develop NCEM. I'm trying out NCEM tool for downstream analysis(the receiver/sender analysis) of 10X visium with cell2location. following this tutorial: https://github.com/theislab/ncem_tutorials/blob/main/tutorials/type_coupling_visium.ipynb e.g. adata ``` AnnData...
**Question** Hello, I tried to apply ncem on DBiT-seq data. I followed the [tutorial](https://github.com/theislab/ncem_benchmarks/blob/main/notebooks/data_preparation/deconvolution/cell2location_human_lymphnode.ipynb) , prepared the expecting input data successfully. `AnnData object with n_obs × n_vars = 20000 ×...
**Question** Hi I want to use NCEM for CODEX data , but I could find any tutorial or how to prepare the data for this type of analysis. Could please...
I am trying to install ncem on my machine: macOS Monterey 12.6.1 pip 22.2.2 from /Users/sei/opt/miniconda3/envs/test-env/lib/python3.8/site-packages/pip (python 3.8) pip install ncem When I do this I get the following error:...