Yijia (Alva) Jiang

Error in .subscript.2ary(x, , j, drop = TRUE) : subscript out of bounds

4

Hello, I am trying to use doubletfinder in seurat v5, and met the following error when running sweep.res.list

Hi, I am trying to run scRNA-scATAC integration. For the label transfer function, is there a way for me to access seurat metadata columns as a variable? For the example,...

Unable to load visium HD data using seurat

1

Hello, I am trying to load visium HD data using the following command: Load10X_Spatial(data.dir = localdir, filename="filtered_feature_bc_matrix.h5") However, my r session is killed. The size of matrix is about 300MB,...

Hello, I am trying to split my spatial transcriptomic data before running deconvolution. However, I got the following error: SpatialRNA: coords, counts, and nUMI do not share any barcode names....

failure to import spatialdata_io

1

Hello, I am running one of the tutorials and I have installed both spatialdata and spatialdata_io packages, but there is an error importing spatialdata_io. Could you help? Thank you very...

Error in scale_color

1

Hello, when using plotnine for ggplot, I get this following error that happens when running this function: class scale_color_cmap(scale_continuous): """ Create color scales using Matplotlib colormaps Parameters ---------- cmap_name :...

Error when running sc.tl.rank_genes_groups

2

### Please make sure these conditions are met - [x] I have checked that this issue has not already been reported. - [x] I have confirmed this bug exists on...

Hello, I am investigating the output of chromVar, and I thought the z-scored deviation score normalizes the deviation score for each motif, and therefore the mean and variance of z-score...

Question about spot filtering in create.RCTD step

1

In create.RCTD step, we can set the threshold for counts_MIN and UMI_min, what is the difference between counts and UMI here? It seems in the restrict_counts function, both refer to...

Error no cell types passed weight threshold on full mode

1

Hello, I received the following error when running RCTD. Could you let me know what might have caused this error? Thank you very much. The code I used is: myRCTD