brgew

Results 28 comments of brgew

Monocl3 BUG！Error in plot_genes_in_pseudotime(cds[genes_sig, ], color_cells_by = "celltype", : unused argument(color_cells_by = "celltype")

Hi, I am unable to reproduce this error. I notice that cell.type rather than celltype is a column in my cds but the different spelling gives a different error message.

Installation problem

Hi, Yes, Monocle3 installs and runs with the latest R, R packages, and Bioconductor packages. You may need to install leidenbase using install.packages('leidenbase')

configure: error: libproj or sqlite3 not found in standard or given locations.

Hi, You need to install the libproj or sqlite3 development object code libraries.

cds <- preprocess_cds(cds, num_dim = 100)

Hi, The discussion in issue # 690 may help. You need to replace both the irlba and Matrix packages, I believe.

Error in cliDef@subclasses : no applicable method for `@` applied to an object of class "NULL"

Hi, I installed Monocle3 and the required packages using R 4.5.0 and I received a similar error. I removed the personal R 'library' and reinstalled everything. This second time the...

❗️R session crashes on preprocess_cds() with both full and subset data

Hi, I cannot reproduce this error. Perhaps, try reinstalling irlba? Or all packages?

Website docs table of contents clipping on mobile browsers

I believe that this is fixed.

reduce_dimension error : address (nil), cause 'memory not mapped'

Hi, You need to run preprocess_cds() before running reduce_dimension().