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muon is a multimodal omics Python framework
Hi there, I think that there is some bug in the count_fragments_features atac features. The gene activity I created from those are very bad looking. This is issue is separate...
when ``` import jax import numpy as np import anndata as ad import muon as mu from muon import MuData z = jax.random.normal(key=jax.random.PRNGKey(1), shape=(100,3)) * jax.numpy.array([2, 3, 4]) w =...
Hi, When trying to write the `mudata` object, `h5py` crashes due to some `.uns` values being `OrderedDict` instead of normal dictionaries. ``` TypeError: No method has been defined for writing...
Hey, I can't seem to find muon on any conda channel. Would suggest to add muon to conda-forge. Cheers
Hi, The documentation for `muon.atac.tl.scan_sequences` (https://muon.readthedocs.io/en/latest/api/generated/muon.atac.tl.scan_sequences.html) does not seem to be up to date. The function's signature and the parameter description do not match. Best GJ
`dsb` normalisation has been implemented in https://github.com/PMBio/muon/pull/9. [The reference implementation](https://github.com/niaid/dsb) now features an updated interface (`DSBNormalizeProtein`), which we should consider to adopt. This should improve user experience when [applying `dsb`...
Hello, thanks for muon! I was trying to reproduce the steps described in the ATAC tutorial (https://muon-tutorials.readthedocs.io/en/latest/single-cell-rna-atac/pbmc10k/2-Chromatin-Accessibility-Processing.html) on my independent dataset, but I get an error from the ac.pl.fragment_histogram function....
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...
**Describe the bug** The `extend_upstream` and `extend_downstream` arguments in [muon.atac.tl.count_fragments_features](https://muon.readthedocs.io/en/latest/api/generated/muon.atac.tl.count_fragments_features.html) do not work as expected because they do not factor in strands. For genes on both strands, the upstream region...
Hi, Is it possible to concatenate two mudata objects. I do not see a method in the reference API. Presently I concatenate two objects separately for each modality using anndata.concatenate...
