RDS File for Mouse Lung

[NicoHadas]

Hello,

Thank you for the tool.

I cannot seem to find the rds file for the Mouse Lung Reference dataset, which limits my ability to use your cellref tool.

Please advise.

[cecilomar6]

Hello,

I had your same issue, and this is how I generated a Seurat file for the Mouse Lung Reference, I hope it helps.

First I downloaded the h5ad file available in LungMAP

Then, I used the SeuratDisk package to convert the h5ad file into h5Seurat and read it:

library(SeuratDisk)

Convert("path/LungMAP_MouseLung_CellRef.v1.h5ad",
        dest = "h5seurat",
        overwrite = FALSE)

ref <- LoadH5Seurat("path/LungMAP_MouseLung_CellRef.v1.h5seurat")

[yuanshuilong]

Hello,

I had your same issue, and this is how I generated a Seurat file for the Mouse Lung Reference, I hope it helps.

First I downloaded the h5ad file available in LungMAP

Then, I used the SeuratDisk package to convert the h5ad file into h5Seurat and read it:

library(SeuratDisk)

Convert("path/LungMAP_MouseLung_CellRef.v1.h5ad",
        dest = "h5seurat",
        overwrite = FALSE)

ref <- LoadH5Seurat("path/LungMAP_MouseLung_CellRef.v1.h5seurat")

Hello! I am trying to use R packages CellRef to annotate my Mouse lung scRNAseq.Now I have successfully downloaded the reference dataset, so next What should i do to use this package to annotate my own dataset? Thank you for your reply

[finn3797]

Hello,
I had your same issue, and this is how I generated a Seurat file for the Mouse Lung Reference, I hope it helps.
First I downloaded the h5ad file available in LungMAP
Then, I used the SeuratDisk package to convert the h5ad file into h5Seurat and read it:

library(SeuratDisk)

Convert("path/LungMAP_MouseLung_CellRef.v1.h5ad",
        dest = "h5seurat",
        overwrite = FALSE)

ref <- LoadH5Seurat("path/LungMAP_MouseLung_CellRef.v1.h5seurat")

Hello! I am trying to use R packages CellRef to annotate my Mouse lung scRNAseq.Now I have successfully downloaded the reference dataset, so next What should i do to use this package to annotate my own dataset? Thank you for your reply

这个项目里面有个示例文件：https://github.com/xu-lab/CellRef/blob/main/vignette/cellref_annotation_demo.html。 照着这个来就可以了。要是要用这个项目鼠的reference的话，把上面的h5ad文件转成h5seurat读到R里面还要跑下PCA。因为这个文件里面pca这个插槽是个空的矩阵，不跑PCA在FindTransferAnchors这一步会报错