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Hello,
I am using `tradeSeq` downstream of `slingshot`. `slingshot` has identified 6 different trajectories, that upon closer inspection seem biologically meaningful.
I wanted to use `tradeSeq` t…
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Hi again,
I followed the jupyter example and found that there are different versions of function to run the VIA; via_wrapper, via.draw_trajectory_gams, or via.VIA etc. I have datasets and want to i…
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when I run:
plot_genes_branched_pseudotime(cds[my_pseudotime_gene,],
branch_point = 1,
color_by = "celltype")
I get:
Warning in class(cellData) != …
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Firstly thanks for adding the transient option!
However, when response_type="transient" i.e. no genes are designated switching svd throws an error:
```
library(ouija)
data(example_gex)
oui
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Hi,
I've encountered several issues running velorama
1. precomputed pseudotime has to be saved in adata.obs['pseudotime'] though scVelo saves it either as dpt_pseudotime or velocity_pseudotime
…
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Hello,
Upon using the plot_genes_in_pseudotime() function, it returns an error similar to this
Error in attributes(out)
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Hi,
thank you very much for providing scMaSigPro. However, I have been trying to use it to analyze some trajectory data produced with Monocle3, but I have been facing two major issues:
1. The Bi…
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hi all
I ran monocle3 passing a Seurat object following the instructions here (https://satijalab.org/signac/articles/monocle.html).
then I wanted to run the DEG analysis but the returned data.f…
SBata updated
2 years ago
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Currently the notebook includes an application on the simulation system from scanpy. The simulation system used in the Scribe paper should also included, ideally full types of data should be included …
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Hi @ctrapnell
Thanks to developing the great tools for pseudotime analysis in singlecell.
I use monocle to make a pseudotime anlysis with my single cell sequencing data. After dimension red…