scverse/scvi-tools

Issues

• Bugs related to MultiVI

  #2949 opened 3 months ago by GoldenCaterpie
  6

• TOTALVI.train() Model training has an invalid value error

  #3028 opened a month ago by raozuming
  0

• Support metric and loss loging on step

  #3020 opened a month ago by Hrovatin
  2

• Inconsistency in covariate injection into layer

  #3021 opened a month ago by Hrovatin
  3

• Cateorical covariate setup

  #3022 opened a month ago by Hrovatin
  2

• Installation jax related packages errs due to deprecations

  #3023 opened a month ago by Hrovatin
  3

• Support training from `AnnCollection`

  #3018 opened a month ago by jacobkimmel
  2

• AttributeError: 'Poisson' object has no attribute 'mu' in POISSONVI get_accessibility_estimates

  #3019 opened a month ago by shahrozeabbas
  1

• Autotune doesn't seem to be able to take learning rate argument anymore

  #3013 opened 2 months ago by LinearParadox
  3

• scvi.model.PEAKVI.setup_anndata(adata): AttributeError: type object 'PEAKVI' has no attribute 'setup_anndata'

  #3008 opened 2 months ago by danli349
  3

• total_vi.train() ValueError: Expected parameter loc (Tensor of shape (256, 20)) of distribution Normal(loc: torch.Size([256, 20]), scale: torch.Size([256, 20])) to satisfy the constraint Real()

  #2981 opened 2 months ago by raozuming
  9

• scvi-tools 1.2.0

  #2889 opened 2 months ago by martinkim0
  4

• Device management

  #2992 opened 2 months ago by canergen
  5

• lightning dependency critical CVE - Update dependency list, especially for conda which is pinned below the CVE patch

  #2941 opened 2 months ago by pranavmishra90
  4

• ValueError: "high is out of bounds for int32" when running setup_anndata on large AnnData object

  #2968 opened 2 months ago by Ron-bio
  10

• installation error when import scvi in conda/pip

  #2955 opened 2 months ago by biobai
  3

• Fix the progress bar during training models trough tout the tutorials

  #2958 opened 2 months ago by ori-kron-wis
  0

• change 1.1.6 release requirements

  #2967 opened 2 months ago by ori-kron-wis
  5

• Drop python 3.9 and replace with python 3.12

  #2966 opened 2 months ago by ori-kron-wis
  0

• potential issue with zinb / nb loss

  #2965 opened 2 months ago by jkobject
  3

• I am getting ZeroDivisionError, any solution in solving this?

  #2963 opened 3 months ago by yojetsharma
  4

• Incompatibility with new anndata 0.10.9

  #2953 opened 3 months ago by mehrankr
  2

• n_proteins Parameter in MultiVI Class

  #2952 opened 3 months ago by GoldenCaterpie
  3

• CellAssign tensor size error

  #2837 opened 3 months ago by andrewjkwok
  9

• Fix custom dataloader registry

  #2907 opened 4 months ago by canergen
  2

• ModelTuner.fit Returns error: The `RunConfig(local_dir)` argument is deprecated.

  #2908 opened 3 months ago by osmanmerdan
  10

• Memory error running CellAssign depending on size of marker gene set reference

  #2935 opened 3 months ago by sjspielman
  8

• error in scanvi_ref

  #2934 opened 3 months ago by AdotaLover
  8

• How to increase num_workers in pytorch DataLoader?

  #2933 opened 4 months ago by winglet0996
  1

• In Jupyter Notebook on Windows, the kernel keeps crashing when running Model hyperparameter tuning with scVI.

  #2917 opened 4 months ago by GLking123
  22

• Reproducibility issue of MRVI

  #2911 opened 4 months ago by justjhong
  4

• autotune throws error for ContrastiveVI (and possibly other external modules)

  #2906 opened 4 months ago by LinearParadox
  1

• Error in model training

  #2909 opened 4 months ago by swasthadinakar
  2

• Use explicit configs instead of kwargs

  #2904 opened 4 months ago by martinkim0
  0

• Expected value argument (Parameter of shape (7150,)) to be within the support (Real()) of the distribution Normal(loc: torch.Size([7150]), scale: torch.Size([7150])), but found invalid values: Parameter containing: tensor([nan, nan, nan, ..

  #2830 opened 4 months ago by Rafael-Silva-Oliveira
  10

• Autotuning with Ray: DeprecationWarning: The `RunConfig(local_dir)` argument is deprecated. You should set the `RunConfig(storage_path)` instead.

  #2895 opened 4 months ago by Rafael-Silva-Oliveira
  2

• How to modify scANVI to handle continuous cell labels?

  #2866 opened 4 months ago by patricks-lab
  1

• Trying to run PeakVI model returns mpi4py error

  #2836 opened 5 months ago by Sun-storm
  2

• AttributeError: module 'numpy' has no attribute 'str'.

  #2851 opened 5 months ago by klshen8386
  5

• Update release checklist and documentation for new release workflow

  #2880 opened 5 months ago by martinkim0
  1

• solo.predict() should take an argument to return Non-softmax transformed values, and return logits like previous iterations to allow for non-breaking change that was implemented in 1.1.3

  #2869 opened 5 months ago by barstuart
  2

• Release 1.1.3

  #2819 opened 5 months ago by martinkim0
  0

• Error in py_call_impl(callable, call_args$unnamed, call_args$named)

  #2849 opened 5 months ago by liuzhuoliang123
  2

• Discussion thread: New DestVI model that supports Visium HD (single-cell spatial transcriptomics) data - Timeline, releases and alternatives

  #2840 opened 5 months ago by Rafael-Silva-Oliveira
  2

• Question about the output of scVI and scANVI

  #2838 opened 5 months ago by ngvananh2508
  2

• Error computing posterior predictive check `calibration_error`

  #2820 opened 5 months ago by jpintar
  1

• Specifying cell types in the new MRVI tool

  #2839 opened 5 months ago by jindalk
  1

• Exception has occurred: ImportError cannot import name 'REGISTRY_KEYS' from 'scvi'

  #2833 opened 5 months ago by Rafael-Silva-Oliveira
  3

• ImportError: cannot import name 'packaging' from 'pkg_resources' for Model Tuning using Ray

  #2814 opened 5 months ago by shahrozeabbas
  4

• Issues in Load Dataset with SeuratData and convert to adata

  #2815 opened 6 months ago by GischD
  2