Emma Dann
Emma Dann
Hello, I am following the vignette for scATAC and scRNA integration and I got stuck in Step 14 (Create a cell-by-peak matrix). I used snaptools to add my cell-by-peak matrix...
Hi there, First of all, every time I go back to working with muon it gets better and better, so thanks for the great work! I was wondering whether you...
Hello, I just found that if I reassign the `var_names` in my object without renaming the `Index` object, I get an error when if I try to save the object...
Noting down issues to fix and potential improvements to milopy, encountered while writing tutorial (https://github.com/theislab/pertpy-tutorials/pull/4) - issues entirely inherited from my code ofc :) `milo.add_covariate_to_nhoods_var` - change name to `add_covariate_to_nhoods_obs`...
Hi there, not sure whether this is really a bug, but if I make certain changes to a `MuData.obs` (e.g. removing duplicate columns), the `obs` in the copy becomes different...
Following discussion with @ivirshup in #144, this is a proposed implementation for a strand-aware `expand` operation, adding the option `direction_col`.
The error: ```py milo.make_nhoods(adata, prop=0.05) ``` ```pytb InvalidIndexError: (array([ 6, 14, 31, 32, 36, 41, 44, 45, 46, 1226, 1893, 2742, 3122, 3475, 3494, 3578, 3588, 4416, 4446, 5146, 5274,...
Gathering some suggestions: - Patsy for model matrix encoding https://patsy.readthedocs.io/en/latest/overview.html - GLM implementation in `pymc3` https://docs.pymc.io/notebooks/GLM-poisson-regression.html
The original cell-level AnnData object and the sample x nhoods AnnData are stored in a common MuData object with `.mod` `cells` and `samples`. Samples are in `mdata["samples"].obs` and nhoods are...
Current implementation gives `KeyError` with missing `Nhood_size`