ZhangHao

This error may be caused by the different **features** or **cells** between assays or slots in the h5Seurat. You can load them separately and check whether has an equal length....

It seems that the file "tmp.h5Seurat" has been opened. You can try deleting the file and run SaveH5Seurat again.

The article has not been published yet, so please cite the SCP repository address and version number. Hope it can help you.

RunPAGA or RunSCVELO use the "RNA" assay as an "X" matrix in [anndata ](https://anndata.readthedocs.io/en/latest/generated/anndata.AnnData.html)by default. I found that your "spliced" assay has 18401 features, which may be a subset of...

I found that feature numbers being different between assays would cause the adata conversion to fail. In the latest version, I have solved this problem. And added the example of...

[scmap](https://bioconductor.org/packages/release/bioc/html/scmap.html) is a Bioconductor package. You can try to install it manually from Bioconductor: ``` options(repos = BiocManager::repositories()) BiocManager::install("scmap") ``` Or install from GitHub: ``` install.packages("devtools") devtools::install_github("hemberg-lab/scmap") ```

I found that ‘harmony’ was removed from the CRAN repository recently. You can install it manually from GitHub. ``` library(devtools) install_github("immunogenomics/harmony") ``` In the next SCP version, I will move...

You may be using an older version of SCP. You can try reinstalling the latest version and running SCP::PrepareVirtualEnv() in a new R session.

Enrichment analysis in SCP calls the available threads by default via `BiocParallel::bpparam()` to speed up the computation. The error seems to be a problem with BiocParallel (Bioconductor/BiocParallel#206, Bioconductor/BiocParallel#189, Bioconductor/BiocParallel#177). I...

I meet the same problem.....