olga

Hello, I ran show.velocity.on.embedding.cor(emb = Embeddings(velo, reduction = "umap"), vel = Tool(velo, slot = "RunVelocity"), n = 200, scale = "sqrt", xlab = colnames(Embeddings(velo, reduction = "umap"))[1], ylab = colnames(Embeddings(velo,...

enrichedheatmap

3

HI, I was trying to plot my enriched heatmap using a normalized matrix. Unfortunately, when I try to plot it, I can see only half of the heatmap plotted. Could...

hi, I'm using rustdesk on linux to another machine with ubunt 22, but I cannot use mouse neither keyboard despite I'm able to connect and see that the computer is...

how to plot the label of genes in 3d plot?

3

I don't understand how to determine if a gene is in the end of trajectory, I have a list of markers of interest. they have highers pseudoorder values. ho can...

is possible to compare conditions?

1

hi, I have a dataset of integrated KO + WT cells. Is it possible to split in some way the trajectories for each condition in R?

Separate two condition and fix the grid

13

Dear all, I have a dataset and I would to split conditions (ko and WT) to analyze separately them. The problem Is that Im not sure if there Is a...

Hi, I have 4 experimental conditions: **WT (2 reps)** **KO1 (2 reps)** **KO2 (2 reps)** **KO3 (2 reps)** I would like to compare the expression of WT against the 3...

HdWGCNA for single Cell ATACseq

1

Hi @smorabit, I would like to know if it is possible to use hdwgcna with single Cell ATAC coverage data instead of the SC RNA-seq expression matrix. How should the...

Split conditions and annotate

3

Hello team I would like to split my dataset by condition and annotate the cell types using SingleR. Is there a way to visualize or compare the differences in cell...

alr t test

3

Hi, what is meant by `alr_t_model.fit_model(reference_cell_type=4)` in the frequentist test? I don't know which cell type to use as a reference. Moreover, when I loop to evaluate the best reference...