aristoteleo/dynamo-release

Issues

• None object in dictionary will be ignored when saving to h5ad

  #561 opened a month ago by Sichao25
  3

• kmc velocity projection method raise ValueError

  #584 opened a month ago by Sichao25
  2

• AI docs assistant

  #590 opened a month ago by Sichao25
  2

• Separate two condition and fix the grid

  #675 opened a month ago by feanaros
  12

• LinAlgError when running dyn.tl.dynamics()

  #676 opened a month ago by nprashant2001
  0

• Bugs when I do not intend to use PCA to infer in-silico perturbation

  #642 opened a month ago by HelloWorldLTY
  4

• bugs in pl.scatters when dealing with large scale datasets (> 1 million points)

  #641 opened 2 months ago by Xiaojieqiu
  1

• Which two layers of dynast are suitable as new and total for scNT-seq？

  #672 opened 3 months ago by mingjianPeng
  1

• Refactor and optimize the tools module

  #478 opened 2 months ago by Sichao25
  2

• Missing documentation for vector_field_function

  #633 opened 2 months ago by Baschdl
  6

• update velocity class to enable cell-wise beta/gamma input

  #545 opened 2 months ago by Xiaojieqiu
  3

• correctly use total RNA or splicing RNA gamma

  #546 opened 2 months ago by Xiaojieqiu
  3

• add an article to summarize the method we developed for estimating kinetic parameters for the labeling data

  #547 opened 2 months ago by Xiaojieqiu
  3

• Most probably path predictions: error message: 'networkx.convert_matrix' has no attribute 'from_scipy_sparse_matrix'

  #673 opened 3 months ago by fengshuoliu
  2

• Can anybody offer an alternative link for downloading hematopoisis tutorial hd5a data?

  #572 opened 3 months ago by US36zcai
  5

• ModuleNotFoundError: No module named 'hnswlib' when running dyn.tl.cell_velocities(adata_hsc_raw)

  #631 opened 3 months ago by Jingle0814
  2

• Missing LinearODE methods in mix_kin_deg and mix_pulse_chase experiments.

  #576 opened 9 months ago by Sichao25
  2

• save h5ad error [TypeError: Can't implicitly convert non-string objects to strings]

  #622 opened 6 months ago by Jingle0814
  10

• Bug on 3D plots

  #608 opened 7 months ago by Sichao25
  1

• Is there a way to run the animate fate transition code block for an in-silico perturbed vector field?

  #655 opened 4 months ago by kousaa
  11

• Error about group parameter in dyn. tl. dynamics

  #670 opened 3 months ago by mingjianPeng
  3

• Automatically generated release notes

  #615 opened 7 months ago by Sichao25
  1

• Further optimize Preprocessor

  #589 opened 8 months ago by Sichao25
  1

• Improvement of Test Files

  #600 opened 7 months ago by Sichao25
  1

• Is there a function that can generate velocity graph, similar to scv.tl.velocity_graph?

  #659 opened 4 months ago by VivLon
  2

• TypeError: 'tuple' object does not support item assignment and AttributeError: 'LeastActionPath' object has no attribute 'action'

  #553 opened 4 months ago by Mingsenli
  13

• Got an AttributeError: 'NoneType' object has no attribute '_get_renderer' when trying to plot

  #574 opened 4 months ago by lijxug
  3

• AttributeError: 'KernelMarkovChain' object has no attribute 'P' in cell_velocities(adata,method='kmc')

  #571 opened 4 months ago by HuangYutong2021
  3

• dyn.pl.kinetic_curves() received wrong `genes` argument

  #583 opened 5 months ago by dyinboisry4u
  3

• ValueError: 'x0' must only have one dimension. when do dyn.pd.least_action()

  #578 opened 5 months ago by dyinboisry4u
  3

• Bug for dyn.pp.recipe_monocle when the normalized data of the gene expression was used

  #523 opened 5 months ago by Mingsenli
  5

• dyn.tl.dynamics error: ... convert to numpy

  #575 opened 7 months ago by zelhar
  4

• Error in gene_wise_confidence correction and confident_cell_velocities correction

  #566 opened 7 months ago by Jordanfink970
  4

• Differences in vector field calculations between different functions

  #472 opened 7 months ago by Fra-Mante
  11

• Improve the read and save of velocity parameters

  #548 opened 8 months ago by Sichao25
  3

• How to generate "X_umap_distances" and "cosine_transition_matrix"

  #544 opened 8 months ago by Mingsenli
  6

• TypeError: unhashable type: 'slice'

  #540 opened 9 months ago by Mingsenli
  3

• what is 'M_u', 'M_uu', 'M_s', 'M_us', 'M_ss' in adata.layer? What do they represent?

  #536 opened 9 months ago by Mingsenli
  4

• Please refer to igraph instead of python-igraph

  #562 opened 9 months ago by szhorvat
  1

• Refactor the preprocessing module

  #465 opened 9 months ago by Sichao25
  4

• dyn.pd.perturbation: TypeError: unsupported operand type(s) for +: 'float' and 'NoneType'

  #481 opened 10 months ago by Mingsenli
  22

• Matplotlib version when installing in a clean conda

  #480 opened 10 months ago by GeorgeAlehandro
  3

• how to get cell wise beta gamma

  #477 opened 10 months ago by changyunjian
  2

• anndata version

  #471 opened a year ago by wangjiawen2013
  3

• fail to import dynamo

  #464 opened a year ago by heyouzhe
  2

• what is the adata.layers['matrix'] ?

  #526 opened a year ago by Mingsenli
  2

• Jacobian

  #517 opened a year ago by smilesw
  1

• Add new methods to select the feature genes in dyn.pl.feature_genes

  #476 opened a year ago by Ukyeon
  1

• I can't install dynamo in M1 MacOS Monterey 12.6. error :bdist_wheel did not run successfully.

  #490 opened a year ago by wangshuo2021
  3

• Measure the impact of "Perturbation"

  #491 opened a year ago by Juneil-Jang
  1