Yufei Chen

You might want to check if any of the cell barcodes ("CB" tag in the .bam file) contain dashes ("-"), since velocyto.py uses dashes to determine barcodes. Reference: https://github.com/velocyto-team/velocyto.py/blob/0963dd2df0ac802c36404e0f434ba97f07edfe4b/velocyto/counter.py#L211-L212

I managed to load the dataset mentioned by @danielruss after transposing the data. ```R Convert("./matrices/allexpsctl.h5ad", "H5Seurat", overwrite = TRUE) obj_HDF5

Unlike ordinary facetting function, `ggbreak` seems to take a different approach to splitting axes, which is incompatible with `ggrepel`. However, you can still use `facet_grid()` with `space = "free_*"` and...

Clearing the local cache of `AnnotationHub` may work: ```R ah

Currently I am using a `repeat` loop to render PDF which contains paginated plots spanning arbitary number of pages. ```R pdf("path_to_pdf.pdf", ...) i

I see. It seems to be fine to modify the value of `page`, as all arguments passed to the faceting function will be stored in `p$facet$params` (including default ones). This...

I discovered that you can get around this by setting `gex_only` to `False` when calling `read_10x_mtx()`: ``` Python adata = sc.read_10x_mtx(path, gex_only = False) ``` However, the warning message persists:...

There is another compatibility issue to consider: When using the latest version of Seurat (v5.1.0), `supercell_2_Seurat` will fail if the `Seurat.object.assay.version` option is unset or is set to `v5`. The...

It happens to me occasionally, I have to manually clean repodata cache every time it get stuck. FYI I am working in an HPC environment where my project data and...

> Removing the binarization in FeaturePlot() like below seems to restore the expected behavior. However, I am not sure when this was changed and if this change has any side-effects....