scFates

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Maximum complexity of trees [question]

2

Hi @LouisFaure I am interested in using scFates to identify the tree of cell populations - but I am concerned about the complexity of the data. How complex can the...

vitkl

Bumps [jinja2](https://github.com/pallets/jinja) from 3.1.3 to 3.1.4. Release notes Sourced from jinja2's releases. 3.1.4 This is the Jinja 3.1.4 security release, which fixes security issues and bugs but does not otherwise...

dependabot[bot]

get a weird figure following the notebook named Bone marrow fates

1

Hi!. I try to show the differentiation trajectory of HSC followed the tutorial. After PCA, diffusion, palantir, I got a unexpected figure. The branch tip cells looks like a string....

huili469r

Hello world! I've starting applying the scFates algorithm to my analysis. I would like to know if it is possibile to change the color of cells in the function of...

pmarzano97

Bumps [jinja2](https://github.com/pallets/jinja) from 3.1.4 to 3.1.6. Release notes Sourced from jinja2's releases. 3.1.6 This is the Jinja 3.1.6 security release, which fixes security issues but does not otherwise change behavior...

dependabot[bot]

Broken tree

1

Hi! Thanks for creating this amazing tool. I was playing with scFates and noticed that scf.pl.graph generated a broken tree, which I suspect is due to clusters being too far...

izu0421

Hi, is it possible to extract the principal tree/curve as an editable svg or eps file? I noticed in Version 0.4.0 February 25, 2022 'Segments and nodes are now rasterized...

felkoh

3 milesones make error in scf.tl.linearity_deviation.

1

To begin with, Thank you for creating such an excellent tool. However, an error occurs in the default code when there are three milestones. Do you have any idea how...

ChaewonKim99

Compatibility Issue with pandas in scFates 1.0.8 while i use tl.test_fork

5

Hi scFates team, I am using scFates version 1.0.8 along with pandas 1.5.3, which is the latest version that satisfies the

Almasimaryam

Pseudotime computation fails when cells_back has fewer columns than boo

10

Hi Louis, When using scFates.tl.pseudotime() with n_map > 100 on complex branching datasets, I consistently encountered the following error:  It appears that `cells_back` has fewer columns than `boo`, due...

tianxin-wang