pyscenic 安装单细胞转录因子分析成功安装`np.object` was a deprecated alias for the builtin `object`. To avoid this

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已于 2023-06-29 20:54:58 修改

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文章标签： python 开发语言

于 2023-05-24 11:12:25 首次发布

本文链接：https://blog.csdn.net/qq_52813185/article/details/130843080

本文提供了pySCENIC的不稳定版本安装方法，包括从源代码克隆并使用pip安装。还提到了在安装过程中遇到的问题，如Numpy的版本问题，以及解决这些问题的步骤，如降级到Numpy1.23.5。此外，还详细列出了loompy、scanpy和其他依赖库的安装命令，包括使用mamba和conda-forge。

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Installation and Usage — pySCENIC latest documentationhttps://pyscenic.readthedocs.io/en/latest/installation.html#installation

Development

You can also install the bleeding edge (i.e. less stable) version of the package directly from the source:

git clone https://github.com/aertslab/pySCENIC.git
cd pySCENIC/
pip install .

Pin numpy until np.object is not used anymore by pcm32 · Pull Request #478 · aertslab/pySCENIC (github.com)https://github.com/aertslab/pySCENIC/pull/478

重新安装Numpy 1.23.5即可

Pining to Numpy 1.23.5 seems to get rid of this, leaving me again in the dask issues, but that is a different story.

conda install mamba  -y -c conda-forge -c bioconda
mamba install loompy -y -c conda-forge -c bioconda
pip install -U loompy -i  https://pypi.douban.com/simple/
mamba install scanpy -c conda-forge -c bioconda -y

pip install pyscenic  -i  https://pypi.douban.com/simple/
pip install --upgrade numpy -i  https://pypi.douban.com/simple/


pip install numpy==1.7 -i  https://pypi.douban.com/simple/