Frequently Asked Questions¶

Here are the answers to some common questions about YOMIX.

How to create embeddings ?¶

Scanpy provides many functions, such as UMAP, PCA, t-SNE, to compute embeddings. See the Scanpy documentation for more details.

You can use Seurat objects by converting them to .h5ad format in R:

Load required libraries:

library(rhdf5)
library(dplyr)
library(patchwork)
library(SeuratDisk)
library(Seurat)
library(SeuratData)

Load the object:

my_file <- readRDS("path.rds")

If it is a SingleCellExperiment object, convert to Seurat:

if (inherits(my_file, "SingleCellExperiment")) {
    my_file <- as.Seurat(my_file)
}

Save as H5Seurat:

SaveH5Seurat(my_file, filename = "filename.h5seurat")

Convert to .h5ad:

Convert("filename.h5seurat", dest = "h5ad", output.path = "/.h5ad")