ENVI
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dpeerlab
Hi, I have a question regarding the input to ENVI. I read in one of [your comments in another issue](https://github.com/dpeerlab/ENVI/issues/4#issuecomment-1997787689) that "Also, make sure the data is not logged (in...
Hi, there is a bug when I follow the readme file to install envi: ``` File /gpfs/gibbs/project/zhao/tl688/conda_envs/envi/lib/python3.9/site-packages/jax/_src/scipy/linalg.py:403 399 del overwrite_b, debug, check_finite # unused 400 return _solve_triangular(a, b, trans, lower,...
Dear developers, I have a question regarding computing niche cell type composition from following tutorial. [https://scenvi.readthedocs.io/en/latest/tutorial/MOp_MERFISH_tutorial.html](tut) I have two spatial dataset where one has corresponding scRNAseq but another one does...
Hey, I just want to use the COVET method to compute niches on spatial data. I have several batches in my data. Should I just use `compute_covet` function with `batch_key`...
Replaced gene-gene covariance representation of spatial niche with a cell-gene expression representation. At inference time, imputes the expression of neighboring cells.
When initializing ENVI, all COVET matrices for all cells in spatial data are computed and held in memory. The COVET matrices must all fit into RAM, which limits the number...
Thank you so much for this interesting package! I was reading through the paper, and you calculate a shifted gene expression covariance matrix. Subsequently, you state you compute the euclidean...
Hello, Thank you for developing ENVI, I think it's a really promising tool! Nevertheless, I have tried out the first version of ENVI with Tensorflow, and the UMAP in the...
Is this algorithm suitable for analyzing 10X Visium data? 50um.
Dear authors, I was running compute_covet on Xenium data for different values of the parameters k and g. According to your paper, obsm["COVET"] should be a tensor of the size...
