Ecosyste.ms: Issues
An open API service for providing issue and pull request metadata for open source projects.
GitHub / scverse/scvi-tools issues and pull requests
#1987 - Refactor dataloaders module
Pull Request -
State: closed - Opened by martinkim0 over 1 year ago
#1986 - Expose keyword arguments for modules
Pull Request -
State: closed - Opened by martinkim0 over 1 year ago
- 1 comment
#1985 - Validate URLs in `scvi.hub`
Pull Request -
State: closed - Opened by martinkim0 over 1 year ago
- 1 comment
#1984 - scvi import error in window
Issue -
State: closed - Opened by jheonsuh over 1 year ago
- 2 comments
Labels: bug
#1983 - Docs organization
Pull Request -
State: closed - Opened by adamgayoso over 1 year ago
- 1 comment
#1982 - myst admonitions for notebooks
Pull Request -
State: closed - Opened by adamgayoso over 1 year ago
- 1 comment
#1981 - dedent devices
Pull Request -
State: closed - Opened by adamgayoso over 1 year ago
- 1 comment
#1980 - Fix adversarial classifier
Pull Request -
State: closed - Opened by adamgayoso over 1 year ago
- 1 comment
#1979 - Posterior probability of scVI/scANVI models
Issue -
State: closed - Opened by TzuTingWei over 1 year ago
- 1 comment
Labels: enhancement, scanvi
#1978 - Deprecate `use_gpu` for `accelerator` and `devices`
Pull Request -
State: closed - Opened by martinkim0 over 1 year ago
- 1 comment
#1977 - Test against Python 3.11
Pull Request -
State: open - Opened by adamgayoso over 1 year ago
- 4 comments
#1976 - Disable default seed
Pull Request -
State: closed - Opened by adamgayoso over 1 year ago
- 1 comment
#1975 - Clean up dataloader, remove `drop_last` as int
Pull Request -
State: closed - Opened by adamgayoso over 1 year ago
- 1 comment
#1972 - when i import scvi i get this error
Issue -
State: closed - Opened by irfan11223344 over 1 year ago
- 6 comments
Labels: bug
#1971 - [pre-commit.ci] pre-commit autoupdate
Pull Request -
State: closed - Opened by pre-commit-ci[bot] over 1 year ago
- 4 comments
#1970 - sphinx autodoc typehints is back, use docrep for de docs
Pull Request -
State: closed - Opened by adamgayoso over 1 year ago
- 1 comment
#1961 - Upgrade to lightning 2.0
Pull Request -
State: closed - Opened by adamgayoso over 1 year ago
- 5 comments
#1959 - Test against lightning 2.0 release candidate
Issue -
State: closed - Opened by adamgayoso over 1 year ago
- 1 comment
#1958 - Track more classification metrics in `SemiSupervisedTrainingPlan` and `ClassifierTrainingPlan`
Issue -
State: closed - Opened by adamgayoso over 1 year ago
Labels: enhancement
#1957 - Library size estimation: changing prior variance and n_hidden
Pull Request -
State: open - Opened by vitkl over 1 year ago
- 2 comments
#1955 - Silence verbose logging during scVI training
Issue -
State: closed - Opened by mxposed over 1 year ago
- 4 comments
Labels: enhancement
#1952 - Add the motif_score method of scBasset in scvi-tools
Issue -
State: closed - Opened by Starlitnightly over 1 year ago
- 2 comments
Labels: enhancement
#1951 - Fix fdr gene tagging when integers in var names/obsm columns
Pull Request -
State: closed - Opened by adamgayoso over 1 year ago
- 3 comments
#1950 - Deprecate `use_gpu` for `accelerator` and `devices`
Pull Request -
State: closed - Opened by martinkim0 over 1 year ago
- 3 comments
#1946 - Add reads to fragments function
Pull Request -
State: closed - Opened by lauradmartens over 1 year ago
- 3 comments
#1940 - Pandas 2.0 compat
Pull Request -
State: closed - Opened by adamgayoso over 1 year ago
- 2 comments
#1939 - Test against pandas 2.0 release candidate
Issue -
State: closed - Opened by adamgayoso over 1 year ago
#1937 - Add MuData support for MultiVI
Pull Request -
State: closed - Opened by martinkim0 over 1 year ago
- 2 comments
#1932 - fix return dist docstring
Pull Request -
State: closed - Opened by adamgayoso over 1 year ago
- 1 comment
Labels: on-merge: backport to 0.20.x
#1929 - Jax install error on Mac M1
Issue -
State: closed - Opened by sjfleming over 1 year ago
- 7 comments
Labels: bug
#1927 - Implement PoissonVI to model scATAC-seq fragment counts
Pull Request -
State: closed - Opened by lauradmartens over 1 year ago
- 1 comment
#1926 - Implement PoissonVI to model scATAC-seq fragment counts
Issue -
State: closed - Opened by lauradmartens over 1 year ago
- 15 comments
Labels: enhancement
#1920 - Add an option to control noise ratio in synthetic data generation
Pull Request -
State: closed - Opened by watiss over 1 year ago
- 1 comment
#1919 - Option to specify train and validation split
Issue -
State: open - Opened by eroell over 1 year ago
- 3 comments
Labels: enhancement
#1915 - stage release 0.20.1
Pull Request -
State: closed - Opened by adamgayoso over 1 year ago
- 1 comment
Labels: on-merge: backport to 0.20.x
#1909 - Patch jax device issues
Pull Request -
State: closed - Opened by adamgayoso over 1 year ago
- 4 comments
#1908 - Patch Jax jit/pjit error
Pull Request -
State: closed - Opened by martinkim0 over 1 year ago
- 1 comment
#1905 - Unable to import scvi
Issue -
State: closed - Opened by ramakrishnanshreya over 1 year ago
- 4 comments
Labels: bug
#1904 - old model failure to load: Unpickle issue ?
Issue -
State: closed - Opened by Nusob888 over 1 year ago
- 3 comments
Labels: bug
#1902 - return sparse 3d matrix for pp samples
Pull Request -
State: closed - Opened by adamgayoso over 1 year ago
- 1 comment
#1894 - Deprecate `use_gpu` in favor of `accelerator` and `devices`
Pull Request -
State: closed - Opened by martinkim0 over 1 year ago
- 2 comments
#1892 - Clean up torch samplers
Issue -
State: closed - Opened by adamgayoso over 1 year ago
Labels: enhancement
#1887 - Expose local_dir as a public property in HubModel
Issue -
State: closed - Opened by adamgayoso over 1 year ago
Labels: enhancement
#1883 - Global seed always set to 0 on import of scvi
Issue -
State: closed - Opened by thomasgaudelet over 1 year ago
- 7 comments
Labels: bug
#1877 - [Hub] Validate training data url in model card
Issue -
State: closed - Opened by adamgayoso over 1 year ago
#1872 - lvmde code
Pull Request -
State: closed - Opened by PierreBoyeau over 1 year ago
- 2 comments
#1866 - Forks cannot pass PR tests due to Hugging Face secret
Issue -
State: closed - Opened by adamgayoso over 1 year ago
Labels: bug
#1860 - Refactor `use_gpu`
Issue -
State: closed - Opened by adamgayoso over 1 year ago
#1859 - Model request: non-negative spatial factorization (NSF)
Issue -
State: open - Opened by aribenjamin over 1 year ago
- 4 comments
Labels: enhancement, new model
#1838 - Implement Jax analog for `scvi.nn`
Pull Request -
State: closed - Opened by martinkim0 over 1 year ago
- 1 comment
#1805 - Fix observed variable detection
Pull Request -
State: closed - Opened by vitkl over 1 year ago
- 3 comments
#1798 - Refactor Lightning logged metrics
Issue -
State: closed - Opened by martinkim0 over 1 year ago
Labels: enhancement, autotune
#1789 - Some suggestion about GNN
Issue -
State: open - Opened by HuangDDU over 1 year ago
- 1 comment
Labels: enhancement
#1786 - Gene names for scvi.data.retina ?
Issue -
State: open - Opened by rangan2510 over 1 year ago
- 2 comments
#1783 - The Kernel crashed while executing training model
Issue -
State: closed - Opened by sailseem over 1 year ago
- 3 comments
Labels: bug
#1781 - Move latent mode init code to latent mode base model
Issue -
State: closed - Opened by adamgayoso over 1 year ago
- 1 comment
#1780 - Implement batch effect normalization
Issue -
State: closed - Opened by martinkim0 over 1 year ago
Labels: enhancement
#1765 - Allow custom train/test/val splits
Issue -
State: open - Opened by adamgayoso over 1 year ago
Labels: enhancement, data
#1721 - scvi-tools autotuning with Ray Tune
Issue -
State: closed - Opened by martinkim0 over 1 year ago
Labels: enhancement
#1718 - scvi-tools Jax support
Issue -
State: open - Opened by martinkim0 over 1 year ago
- 3 comments
Labels: enhancement, help wanted, new model, dependencies, meta, jax
#1706 - Make DataSplitter more transparent to the existing Lightning Data Loader API wrt kwargs
Pull Request -
State: closed - Opened by mkarikom almost 2 years ago
- 5 comments
#1673 - Switch to sphinx book theme
Pull Request -
State: closed - Opened by adamgayoso almost 2 years ago
- 2 comments
#1634 - gimVI gene imputation error
Issue -
State: closed - Opened by giovp almost 2 years ago
- 4 comments
Labels: bug
#1632 - SCVI Does Not Use a Conditional VAE by Default
Issue -
State: closed - Opened by valentinwust almost 2 years ago
- 7 comments
Labels: bug
#1616 - New defaults
Issue -
State: closed - Opened by watiss almost 2 years ago
- 1 comment
Labels: enhancement, help wanted
#1613 - Improve documentation on `batch_key` vs `categorical_covariate_keys`
Issue -
State: closed - Opened by justjhong almost 2 years ago
- 2 comments
Labels: bug
#1610 - DestVI log-variational for Vamp_prior
Issue -
State: closed - Opened by canergen almost 2 years ago
Labels: bug
#1608 - Basic JaxPEAKVI class
Pull Request -
State: closed - Opened by RK900 almost 2 years ago
- 2 comments
Labels: jax
#1592 - Error module 'scvi.data' has no attribute 'setup_anndata'
Issue -
State: closed - Opened by ccruizm about 2 years ago
- 2 comments
Labels: bug
#1591 - DestVI changed l1 loss. Expected proportions
Pull Request -
State: open - Opened by canergen about 2 years ago
- 3 comments
#1590 - Error when updating format
Issue -
State: closed - Opened by ccruizm about 2 years ago
- 5 comments
Labels: bug
#1587 - Stochastic/Non-deterministic prediction for scANVI
Issue -
State: closed - Opened by akira-nair about 2 years ago
- 2 comments
Labels: enhancement, scanvi
#1584 - Default Jax seed to `scvi.settings.seed`
Issue -
State: closed - Opened by justjhong about 2 years ago
- 1 comment
Labels: enhancement
#1555 - update versions of pytorch lightning, jinja, sphinx
Pull Request -
State: closed - Opened by adamgayoso about 2 years ago
- 4 comments
#1532 - Fix `loss_kwargs` in `AdversarialTrainingPlan`
Pull Request -
State: closed - Opened by justjhong about 2 years ago
- 4 comments
#1530 - batch specific dropout
Pull Request -
State: closed - Opened by adamgayoso about 2 years ago
#1511 - Allow additional arguments for SCVI encoder and decoder
Pull Request -
State: closed - Opened by Koncopd about 2 years ago
- 4 comments
#1510 - Activation functions other than ReLU
Issue -
State: closed - Opened by Koncopd about 2 years ago
- 4 comments
Labels: enhancement
#1485 - OpenVINO backend
Issue -
State: closed - Opened by likholat over 2 years ago
- 2 comments
Labels: enhancement
#1477 - Lightning 1.6 official
Pull Request -
State: closed - Opened by adamgayoso over 2 years ago
- 2 comments
#1464 - Importerror for scVI in tutorials
Issue -
State: closed - Opened by Zethson over 2 years ago
- 21 comments
Labels: bug
#1462 - Refactor tests
Issue -
State: closed - Opened by adamgayoso over 2 years ago
Labels: refactor, tests
#1360 - `DEMixin` module
Pull Request -
State: closed - Opened by PierreBoyeau over 2 years ago
- 2 comments
#1314 - integrate with Lightning ecosystem CI
Issue -
State: closed - Opened by pl-ghost over 2 years ago
- 1 comment
Labels: enhancement
#1293 - Implement VITAE
Issue -
State: closed - Opened by adamgayoso over 2 years ago
Labels: enhancement, help wanted, new model
#1226 - Multi GPU training
Issue -
State: closed - Opened by adamgayoso over 2 years ago
- 20 comments
Labels: enhancement
#1185 - Implement scHPF
Issue -
State: closed - Opened by adamgayoso almost 3 years ago
- 3 comments
Labels: new model
#1184 - Implement Prescient
Issue -
State: closed - Opened by adamgayoso almost 3 years ago
- 3 comments
Labels: help wanted, new model
#1177 - User guide: gimVI
Issue -
State: open - Opened by adamgayoso almost 3 years ago
Labels: user guide
#1167 - LDA Incremental Updates
Issue -
State: closed - Opened by justjhong almost 3 years ago
- 1 comment
Labels: enhancement
#1160 - Jupyter Notebooks need to be run/tested locally or during CI
Issue -
State: closed - Opened by watiss almost 3 years ago
- 2 comments
Labels: enhancement
#1147 - Lightning Tutorials
Issue -
State: closed - Opened by tchaton almost 3 years ago
- 3 comments
Labels: enhancement
#1142 - Add support for DDP.
Pull Request -
State: closed - Opened by tchaton almost 3 years ago
- 1 comment
#1063 - dataloader which stratifies train-validation split by adata.obs columns
Issue -
State: open - Opened by vitkl about 3 years ago
- 8 comments
Labels: enhancement, data
#1052 - Fast nb when data known to be sparse
Pull Request -
State: closed - Opened by adamgayoso about 3 years ago
- 1 comment
#991 - Module tutorial should discuss LossRecorder
Issue -
State: closed - Opened by adamgayoso over 3 years ago
Labels: tutorials
#844 - Version 0.8.0
Pull Request -
State: closed - Opened by adamgayoso over 3 years ago
- 1 comment
#824 - AttributeError: module 'scvi' has no attribute 'data'
Issue -
State: closed - Opened by aralbright over 3 years ago
- 28 comments
Labels: bug
#823 - DE on data subset
Issue -
State: closed - Opened by chenlingantelope over 3 years ago
- 5 comments
Labels: bug
#661 - add random state functionality
Issue -
State: closed - Opened by adamgayoso about 4 years ago
Labels: enhancement