AutoGeneS
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theislab
Dear developers, Thanks for this awesome tool! I am trying to build the signature matrix from microRNA sequencing data from sorted cell populations, but the tutorial was only for single-cell...
Hi Hana, Do you have a documentation for AutoGeneS+? I optimized my single cell data of 13 cell types and found highly correlated cell types. I ran the optimization on...
Dear Author, Thanks for this new API. As you mentioned in your paper, the paragraph of **Hierarchical optimization for highly correlated cell types**. "we ran AutoGeneS separated CD4+ and CD8+...
Hi developers, Thanks for a great tool! I was wondering if you could extract the Reference Profile prior to the actual deconvolution. I am currently trying to make the deconvolution...
Hello, I have a very basic question! After running the "init" and "optimize" steps, I obtain the coefficients with the deconvolve function: ``` ag.init(adata, celltype_key='Celltype') ag.optimize(ngen=5000, nfeatures=400, seed=0, mode="fixed") coef=ag.deconvolve(bulk_data,...
With pip versions > 24 this requirement specification is not valid anymore so installation fails. Only older pip versions allow the installation of autogenes at the moment. https://github.com/theislab/AutoGeneS/blob/22bde0d5eba013e90edb85341e0bd9c28b82e7fd/requirements.txt#L9
