MuDataSeurat

This is a fork from PMBio's MuDataSeurat

Please refer to the original repo for more details

Why this fork ?

I find MuDataSeurat to be the most compatible tool for converting SeuratObject to H5AD/H5MU format. It does not require python runtime as well.

The original repository activity seems quite low, and unfortunately, the bugs have not been fixed promptly. Since I use MuDataSeruat quite often, I've decided to create my own fork and make my own version. I will do my best to ensure that it remains compatible with the latest pull requests from the original repository.

New features

1. Compatible with Seurat v5
2. Tested and works with anndata (>=0.8), and anndata-rs(>=0.2.0).
3. Export all missing reductions, such as UMAP, tSNE etc.
4. Fixed stack overflow issue because of obs column containing NAs
   • skip columns with all NA value
   • fixed string array with NA
5. Add two new keyword arguments to WriteH5AD and WriteH5MU:
   • scale.data: whether write scale.data to anndata/mudata or not.
   • sparse.type: store csc_matrix or csr_matrix in anndata/mudata
6. Correctness fixes
   • .h5mu files are now readable by mudata: obsm, varm, obsp, varp, obsmap and varmap are always written.
   • Categorical (factor) columns keep their labels when a category is unused.
   • NA in string columns is stored as a missing value (as categorical, since anndata has no nullable-string encoding) instead of the text "NaN".
   • WriteH5AD now errors on an unknown assay instead of silently writing a different one.
   • Reductions whose names contain non-alphanumeric characters (umap_harmony, pca_uncorrected, mrVI_umap, ...) are no longer dropped from obsm. Seurat strips those characters when it derives a reduction key (umap_harmony -> umapharmony_), which previously made such reductions fail the assay-matching check and be skipped silently. A reduction that is still not matched now raises a warning instead of disappearing.

Installation

Please install the main branch

remotes::install_github("zqfang/MuDataSeurat")

Usage

Export to H5AD, H5MU

MuDataSeurat only export 3 layers: count, data, scale.data

Therefore, You need JoinLayers for each modality first with seurat v5.

library(MuDataSeurat)

DefaultAssay(seu) = "RNA"
seu = JoinLayers(seu) # critical for seurat v5

## write unimodal h5ad
WriteH5AD(seu, "export.h5ad",  assay="RNA", scale.data = FALSE, overwrite=TRUE)

## write multimodal h5mu
WriteH5MU(seu, "export.h5mu", overwrite=TRUE)

Read H5AD to Seurat

seu <- ReadH5AD("export.h5ad")
seu <- ReadH5MU("export.h5mu")

You may also use the native support of anndata in R: anndataR::read_h5ad