Marwan

AttributeError: 'BayesNet' object has no attribute 'train_stats'

2

i am trying to run MOFA on my mudata object and i run to this issue ``` MuData object with n_obs × n_vars = 2 × 698441 var: 'mean', 'total',...

comparing classic umap and topometry

2

sorry if my question is naive but its for better understanding 1-in a classical workflow, if i use Topometry, is the eigncomponents here considered the dimensionality reduction method? 2- for...

Map projection looks odd with high number of cells

1

Sorry for Bothering again, but after testing on my entire dataset not just 1 sample, around 3/4 million cell, i observe this MAP projection and am not sure what could...

paCMAP generate an error ,

1

using same code with MAP projecion works fine > projections=["MAP"] `tg = tp.TopOGraph(n_eigs=119, n_jobs=-1, verbosity=0) tg.run_models(adata.X, kernels=['bw_adaptive'], eigenmap_methods=['msDM'], projections=["PaCMAP"]) --------------------------------------------------------------------------- ValueError Traceback (most recent call last) Cell In[65], line 3...

problem with the Delayed Array matrix

1

hey, i generated a sce object using readH5AD with big object and i am failing to convert it the delayed matrix to dgCMatrix or CsparseMatrix and i wanted to ask...

cannot convert DelayedMatrix format for big sce object

1

Hey i am failing to convert the delayed matrix to dgCMatrix or CsparseMatrix for a big matrix file. noting that the same code work for a subset of 10k cells...

interpreting the output with the issue of compositionality.

6

I am trying to get my head around the compositionality issue and i would like to ask 2 questions, 1)using poisson regression and wilcoxon rank sum test i can see...

Using continuous variables yield weird results.

3

Hi, I'm experiencing issues with scCODA when analyzing the effect of a continuous covariate (CMV serostatus) as opposed to a categorical one. When I categorize CMV serostatus as positive/negative based...

Liana on pseduo bulk-sc data data

6

Hey, I want to know if it's best practice to always use single cell data on liana to compute the l-r ccc results, as I saw in the tutorial of...

scCODA convergence issue for continous covairables

2

Hey, I'm experiencing issues with scCODA when analyzing the effect of a continuous covariate (like age for ex ) as opposed to a categorical ones . using continuous values yields...