-
I was trying to carte lineage tree and calculate branch probabilities with mira.time.get_branch_probabilities using terminal cells detected from mira.time.find_terminal_cells. I got the error of "LinA…
-
Hello!
I've been using the plot_genes_branched_pseudotime and plot_multiple_branches_pseudotime functions to plot the trends of selected genes after a branching point. It appears the scaling for ge…
-
**I run cd.pseudo_time() same as that in the Case study 1:**
import random
dt = 0.05
t_total = {dt:int(10/dt)}
n_repeats = 10
cellDancer_df_update = cd.pseudo_time(cellDancer_df=cellDancer_df,
…
-
Hi Dr. Hou, it's great to have an alternative to try in relation to tradeseq - I thought the paper was clear and an interesting read. I was wondering what expected runtimes may be for the lamian_test …
-
To do:
* [ ] Diffusion Pseudotime
* [x] Slingshot (needs R interface)
-
Hi All,
I am trying to use Monocle3 as input to tradeSeq. But i met following error:
sce
-
Hi,
when I run the function of plot_genes_in_pseudotime, it showed the error below:
Error in attributes(out)
-
Hi,
I've obtained single-cell NGS data of "non-model" organism (plants) and want to cluster the cells in pseudotime, subsequently to estimate a phase transition along with pseudotime. I need an un…
-
I tried this:
> plot_genes_branched_pseudotime(HSMM_major[84,], branch_point = 1,color_by = "cell_class", ncol = 2)
and got this error:
Error in if (nrow(ancestor_exprs) == 1) exprs_data
-
Here is an example header lines for the PseudoTime.csv file in the Curated GSD inputs:
```
,PseudoTime1,PseudoTime2
E801_438,,0.54762
E1_769,,0.96241
E1795_733,0.9172899999999999,
E645_767,,0.95…