Laura Martens

Change order of chromosomes

5

Hi, I processed my HiC data using HiC-Pro but unfortunately the chromosomes were in a weird order. I was wondering if there is a way to change the order of...

**Describe the bug** The `muon.atac.tl.count_fragments_features` function uses the score in the fragment file to count fragments: https://github.com/scverse/muon/blob/31a45d76f7a1d97eee34866e525788f960e7d504/muon/_atac/tools.py#L860 This score also includes all duplicated read pairs: https://support.10xgenomics.com/single-cell-atac/software/pipelines/latest/output/fragments, but we only want...

Read bam with split reads

5

Hi, first of all thanks a lot for this great tool! I was wondering if it would be possible to have the make fragment files function from bam files also...

Poissonmultivi

3

Hi @martinkim0, I had some time and added the Poisson loss also to the MultiVI model (POISSONMULTIVI) to the external models. Addresses #2257 for Poisson likelihood.

Conversion of seqlevel styles

2

### Description of feature Add functionality that allows translation between different chromosome sequence naming conventions (e.g., "chr1" versus "1"). This could be similar to the `seqlevelsStyle` function in the [R...

Fix for get_normalized_expression

1

There is currently a problem when using the scvi model with `gene_likelihood='poisson'` and trying to get the normalized expression: ``` vae = scvi.model.SCVI( adata, gene_likelihood='poisson' ) vae.get_normalized_expression( adata=adata, library_size="latent", )...