Questions tagged [monocle]

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how to change the pseudo time trajectory direction?

Monocle is a comprehensive bioinformatics package which has the function to run the pseudo-time trajectory and changes in direction. I wish to replicate this analysis. Like in the figure I would like ...
cow's user avatar
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2 answers
641 views

How to find differential expressed genes within pseudotime trajectory with Seurat cluster?

Did anyone know how to find the differential expressed genes within pseudotime trajectory with Seurat cluster? In monocle tutorial, we can use BEAM to find the differential expressed genes between the ...
hua's user avatar
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2 votes
1 answer
298 views

Pseudotime analysis on multiple samples

I am using Monocle3 to run pseudo time analysis on samples at two different conditions (samples are paired). My question is, is it valid to combine all the cells ...
Ahmed Elhossiny's user avatar
1 vote
1 answer
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Is there a difference between any scRNA-seq visualization and pseudotime?

Is there a good definition of pseudotime? Some tools are clearly labeled as pseudotime and produce values along a trajectory, but there are more complex approaches that involve branching and ...
burger's user avatar
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1 answer
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how to export the monocle data into Seurat

I have tried to export the monocle data into Seurat and got the error ...
hua's user avatar
  • 441