scverse/scvi-tools issues and pull requests

#1935 - MultiVI changes

Issue - State: open - Opened by martinkim0 over 1 year ago
Labels: enhancement, multivi

#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 almost 2 years ago - 4 comments

#1908 - Patch Jax jit/pjit error

Pull Request - State: closed - Opened by martinkim0 almost 2 years ago - 1 comment

#1906 - library_size argument not used fully in TOTALVI get_normalized_expression

Issue - State: open - Opened by deto almost 2 years ago
Labels: totalvi, P1

#1905 - Unable to import scvi

Issue - State: closed - Opened by ramakrishnanshreya almost 2 years ago - 4 comments
Labels: bug

#1904 - old model failure to load: Unpickle issue ?

Issue - State: closed - Opened by Nusob888 almost 2 years ago - 3 comments
Labels: bug

#1903 - `use_observed_lib_size=False` fails with NaN for some datasets

Issue - State: open - Opened by vitkl almost 2 years ago - 6 comments
Labels: bug, nan, P0

#1902 - return sparse 3d matrix for pp samples

Pull Request - State: closed - Opened by adamgayoso almost 2 years ago - 1 comment

#1894 - Deprecate `use_gpu` in favor of `accelerator` and `devices`

Pull Request - State: closed - Opened by martinkim0 almost 2 years ago - 2 comments

#1892 - Clean up torch samplers

Issue - State: closed - Opened by adamgayoso almost 2 years ago
Labels: enhancement

#1887 - Expose local_dir as a public property in HubModel

Issue - State: closed - Opened by adamgayoso almost 2 years ago
Labels: enhancement

#1883 - Global seed always set to 0 on import of scvi

Issue - State: closed - Opened by thomasgaudelet almost 2 years ago - 7 comments
Labels: bug

#1877 - [Hub] Validate training data url in model card

Issue - State: closed - Opened by adamgayoso almost 2 years ago

#1872 - lvmde code

Pull Request - State: closed - Opened by PierreBoyeau almost 2 years ago - 2 comments

#1866 - Forks cannot pass PR tests due to Hugging Face secret

Issue - State: closed - Opened by adamgayoso almost 2 years ago
Labels: bug

#1860 - Refactor `use_gpu`

Issue - State: closed - Opened by adamgayoso almost 2 years ago

#1859 - Model request: non-negative spatial factorization (NSF)

Issue - State: open - Opened by aribenjamin almost 2 years ago - 4 comments
Labels: enhancement, new model, backlog

#1840 - Finalize scBasset

Issue - State: open - Opened by adamgayoso almost 2 years ago - 4 comments
Labels: enhancement, help wanted, backlog

#1838 - Implement Jax analog for `scvi.nn`

Pull Request - State: closed - Opened by martinkim0 almost 2 years ago - 1 comment

#1826 - Spatial deconv models from rna model should also work with paths

Issue - State: open - Opened by adamgayoso almost 2 years ago
Labels: spatial, P1

#1817 - scvi-hub enhancements

Issue - State: closed - Opened by watiss almost 2 years ago
Labels: enhancement, hub

#1805 - Fix observed variable detection

Pull Request - State: closed - Opened by vitkl almost 2 years ago - 3 comments

#1801 - Posterior sampling with Messenger Pyro guides -> huge memory use.

Issue - State: open - Opened by vitkl almost 2 years ago - 5 comments
Labels: bug, pyro, P1

#1798 - Refactor Lightning logged metrics

Issue - State: closed - Opened by martinkim0 about 2 years ago
Labels: enhancement, autotune

#1789 - Some suggestion about GNN

Issue - State: open - Opened by HuangDDU about 2 years ago - 3 comments
Labels: enhancement, data, P2

#1786 - Gene names for scvi.data.retina ?

Issue - State: open - Opened by rangan2510 about 2 years ago - 2 comments

#1784 - Loss formulation in SCANVI

Issue - State: open - Opened by haoyang-insitro about 2 years ago - 5 comments
Labels: bug, scanvi, P2

#1783 - The Kernel crashed while executing training model

Issue - State: closed - Opened by sailseem about 2 years ago - 3 comments
Labels: bug

#1781 - Move latent mode init code to latent mode base model

Issue - State: closed - Opened by adamgayoso about 2 years ago - 1 comment

#1780 - Implement batch effect normalization

Issue - State: closed - Opened by martinkim0 about 2 years ago
Labels: enhancement

#1765 - Allow custom train/test/val splits

Issue - State: closed - Opened by adamgayoso about 2 years ago - 1 comment
Labels: enhancement, good first issue, data, P0

#1744 - Manager summary stats should be per field

Issue - State: open - Opened by adamgayoso about 2 years ago - 3 comments
Labels: AnnDataManager, backlog

#1721 - scvi-tools autotuning with Ray Tune

Issue - State: closed - Opened by martinkim0 about 2 years ago
Labels: enhancement

#1718 - scvi-tools Jax support

Issue - State: open - Opened by martinkim0 about 2 years ago - 3 comments
Labels: enhancement, new model, meta, jax, P1

#1706 - Make DataSplitter more transparent to the existing Lightning Data Loader API wrt kwargs

Pull Request - State: closed - Opened by mkarikom about 2 years ago - 5 comments

#1673 - Switch to sphinx book theme

Pull Request - State: closed - Opened by adamgayoso about 2 years ago - 2 comments

#1640 - additive effects for background RNA correction in scVI

Issue - State: closed - Opened by vitkl over 2 years ago - 5 comments
Labels: enhancement, P2

#1634 - gimVI gene imputation error

Issue - State: closed - Opened by giovp over 2 years ago - 4 comments
Labels: bug

#1632 - SCVI Does Not Use a Conditional VAE by Default

Issue - State: closed - Opened by valentinwust over 2 years ago - 7 comments
Labels: bug

#1620 - Jax analog for FCLayers

Issue - State: closed - Opened by RK900 over 2 years ago
Labels: enhancement, good first issue, jax, P1

#1616 - New defaults

Issue - State: closed - Opened by watiss over 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 over 2 years ago - 2 comments
Labels: bug

#1610 - DestVI log-variational for Vamp_prior

Issue - State: closed - Opened by canergen over 2 years ago
Labels: bug

#1608 - Basic JaxPEAKVI class

Pull Request - State: closed - Opened by RK900 over 2 years ago - 2 comments
Labels: jax

#1592 - Error module 'scvi.data' has no attribute 'setup_anndata'

Issue - State: closed - Opened by ccruizm over 2 years ago - 2 comments
Labels: bug

#1591 - DestVI changed l1 loss. Expected proportions

Pull Request - State: closed - Opened by canergen over 2 years ago - 3 comments

#1590 - Error when updating format

Issue - State: closed - Opened by ccruizm over 2 years ago - 5 comments
Labels: bug

#1587 - Stochastic/Non-deterministic prediction for scANVI

Issue - State: closed - Opened by akira-nair over 2 years ago - 2 comments
Labels: enhancement, scanvi

#1586 - Model creation fixtures

Issue - State: open - Opened by RK900 over 2 years ago
Labels: bug, backlog

#1584 - Default Jax seed to `scvi.settings.seed`

Issue - State: closed - Opened by justjhong over 2 years ago - 1 comment
Labels: enhancement

#1578 - Implementation of PeakVI in Jax

Issue - State: open - Opened by justjhong over 2 years ago
Labels: new model, jax, P2

#1577 - Support to build NumPyro models.

Issue - State: open - Opened by justjhong over 2 years ago
Labels: enhancement, jax, backlog

#1568 - [TOTALVI] NaN values during training when `empirical_protein_background_prior=True`

Issue - State: closed - Opened by justjhong over 2 years ago - 4 comments
Labels: bug, nan, P0

#1555 - update versions of pytorch lightning, jinja, sphinx

Pull Request - State: closed - Opened by adamgayoso over 2 years ago - 4 comments

#1553 - Granular device management for Jax

Issue - State: open - Opened by justjhong over 2 years ago - 1 comment
Labels: enhancement, good first issue, jax, P1

#1549 - Labels Key in totalVI

Issue - State: open - Opened by StefanMDPhD over 2 years ago - 4 comments
Labels: enhancement, totalvi, P2

#1545 - scANVI classification uncertainty extraction method

Issue - State: closed - Opened by LuckyMD over 2 years ago - 3 comments
Labels: enhancement, scanvi

#1532 - Fix `loss_kwargs` in `AdversarialTrainingPlan`

Pull Request - State: closed - Opened by justjhong over 2 years ago - 4 comments

#1530 - batch specific dropout

Pull Request - State: closed - Opened by adamgayoso over 2 years ago

#1511 - Allow additional arguments for SCVI encoder and decoder

Pull Request - State: closed - Opened by Koncopd over 2 years ago - 4 comments

#1510 - Activation functions other than ReLU

Issue - State: closed - Opened by Koncopd over 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

#1456 - Within cluster DE test

Issue - State: open - Opened by zoesteier over 2 years ago - 2 comments
Labels: enhancement, good first issue, differential expression, P2

#1360 - `DEMixin` module

Pull Request - State: closed - Opened by PierreBoyeau almost 3 years ago - 2 comments

#1314 - integrate with Lightning ecosystem CI

Issue - State: closed - Opened by pl-ghost almost 3 years ago - 1 comment
Labels: enhancement

#1293 - Implement VITAE

Issue - State: closed - Opened by adamgayoso almost 3 years ago
Labels: enhancement, help wanted, new model

#1226 - Multi GPU training

Issue - State: closed - Opened by adamgayoso about 3 years ago - 20 comments
Labels: enhancement

#1185 - Implement scHPF

Issue - State: closed - Opened by adamgayoso about 3 years ago - 3 comments
Labels: new model

#1184 - Implement Prescient

Issue - State: closed - Opened by adamgayoso about 3 years ago - 3 comments
Labels: help wanted, new model

#1177 - User guide: gimVI

Issue - State: open - Opened by adamgayoso about 3 years ago
Labels: user guide, P1

#1176 - User guide: Counterfactuals

Issue - State: closed - Opened by adamgayoso about 3 years ago - 2 comments
Labels: user guide, P1

#1167 - LDA Incremental Updates

Issue - State: closed - Opened by justjhong about 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 about 3 years ago - 2 comments
Labels: enhancement

#1147 - Lightning Tutorials

Issue - State: closed - Opened by tchaton about 3 years ago - 3 comments
Labels: enhancement

#1142 - Add support for DDP.

Pull Request - State: closed - Opened by tchaton about 3 years ago - 1 comment

#1091 - extend history when train method run multiple times

Pull Request - State: closed - Opened by adamgayoso over 3 years ago - 1 comment

#1090 - refactor place where indices are sampled for DE

Pull Request - State: closed - Opened by PierreBoyeau over 3 years ago - 2 comments

#1086 - scANVI predict method should return observed labels instead of predicted

Issue - State: closed - Opened by adamgayoso over 3 years ago - 1 comment
Labels: enhancement, scanvi

#1085 - logging simulated doublets lib size

Pull Request - State: closed - Opened by njbernstein over 3 years ago - 2 comments

#1083 - Parallelizable differential expression

Issue - State: closed - Opened by Munfred over 3 years ago - 1 comment
Labels: enhancement, differential expression

#1082 - Update minimum Python version

Pull Request - State: closed - Opened by adamgayoso over 3 years ago - 1 comment

#1079 - fix scANVI max_epochs bug when pretrained

Pull Request - State: closed - Opened by galenxing over 3 years ago - 1 comment

#1078 - classifier kwargs and fix adata option for solo

Pull Request - State: closed - Opened by adamgayoso over 3 years ago - 3 comments

#1076 - adding ability to get scores for simulated doublets

Pull Request - State: closed - Opened by njbernstein over 3 years ago - 1 comment

#1074 - modify DE results dataframe to have columns "group1" and "group2" in addition to "comparison"

Pull Request - State: closed - Opened by Munfred over 3 years ago - 5 comments

#1073 - adding validation ELBO loss for pyro models

Issue - State: closed - Opened by vitkl over 3 years ago - 3 comments
Labels: enhancement, pyro, P2

#1072 - fix transform batch for models that encode covs

Pull Request - State: closed - Opened by adamgayoso over 3 years ago - 1 comment

#1071 - Pyro logging elbo

Pull Request - State: closed - Opened by adamgayoso over 3 years ago - 1 comment

#1070 - Revert "add warning if current device and train device mismatch"

Pull Request - State: closed - Opened by adamgayoso over 3 years ago - 1 comment

#1066 - Adding ability to change doublet ratios

Pull Request - State: closed - Opened by njbernstein over 3 years ago - 1 comment

GitHub / scverse/scvi-tools issues and pull requests