Ali Asgher Ali

I was wondering if anyone could help me here: I managed t oloadmy tsne coordinates but ran into an issue when I open the loom file and try to set...

Merging: Error in names(model.list) <- all.levels : attempt to set an attribute on NULL

4

Similar to #8186 which worked but now I am running into an error: I have 2 rounds of QC (identified using RQC and RQC2) and I want to compare a...

Code: ``` scrub = scr.Scrublet(counts_matrix, expected_doublet_rate=0.05) #range is 0.05-0.1. doublet_scores, predicted_doublets = scrub.scrub_doublets(min_counts=2, min_cells=3, min_gene_variability_pctl=85, n_prin_comps=100, #set high since this is what I plan to use in Seurat log_transform='TRUE') scrub.set_embedding('UMAP',...

ScaleData " 'qr' and 'y' must have the same number of rows"

1

I get the following error in trying to scale my data, but I do not know why since I have copied this code from another R workbook where it did...

Cross posting: Hello, I have a question about the computational order of operations that I have: I have 10X Multiome experiments (8 samples) of ATAC and GEX. I already merged,...

runSCENIC_4 thresholds not selected for AUCell::AUCell_plotTSNE

1

Hello everyone, I want to adjust my binarisation thresholds. I have the following code from the vignette: ``` #binarize aucellApp

Same issue as #8 I downloaded the file from the [linarson's website ](http://mousebrain.org/development/downloads.html) using HybISS spatial expression data: load_mousebrain_data("/home/ali/Dokumente/voxhunt_mousedata/") ``` Error in x$exists(name) : HDF5-API Errors: error #000: ../../../src/H5L.c in...

[BUG] grnboost2 TypeError: Must supply at least one delayed object

6

**Describe the bug** Running GRNBoost2 produces an error at the very last step. Reproducible with the tutorial (https://pyscenic.readthedocs.io/en/latest/tutorial.html) using the GSE60361_C1-3005-Expression.txt dataset. Installing arboreto from source did not help **Steps...