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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

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

ReadH5AD()
ReadH5MU()

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