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1366409175 wants to merge 96 commits intoTeichlab:masterTeichlab/SpatialDE:masterfrom PMBio:masterPMBio/SpatialDE:masterCopy head branch name to clipboard

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Commits on Jan 15, 2020

• fix s2_t_hat calculation

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Commits on Jan 29, 2020

• First port of SpatialDE to gpflow + tensorflow

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• remove apparently unused file

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Commits on Feb 11, 2020

• fix s2_t_hat calculation

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• remove apparently unused file

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Commits on Mar 5, 2020

• add option to use score test instead of LRT test

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• Merge branch 'master' of https://github.com/ilia-kats/SpatialDE

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Commits on Mar 17, 2020

• do not fit multiple GPs for multiple kernels

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Commits on Mar 18, 2020

• enable pickling of frozen models, improve power spectrum plot

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• fix deleted function in __init__.py

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Commits on Mar 20, 2020

• implement an optimizer based on tensorflow probability, add some minor

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Commits on Mar 23, 2020

• full refactor

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Commits on Mar 24, 2020

• minor bugfixes

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Commits on Mar 27, 2020

• refactor score tests in prepration for NB null model

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Commits on Mar 30, 2020

• testing negative binomial null model

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• performance: perform score test once per gene and model

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Commits on Mar 31, 2020

• Merge branch 'gpflow'

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• fix up some merge issues

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Commits on Apr 6, 2020

• fully integrate gpflow into spatialde

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Commits on Apr 8, 2020

• robustify against singular matrices, some bugfixes

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Commits on Apr 14, 2020

• NB score test: use proper MLE for mean and dispersion

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• clean up obsolete functions

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• setup: bump version, add gpflow dependency

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• remove deleted function from __init__.py

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Commits on Apr 15, 2020

• increase minimum lengthscale for automatically generated kernel space

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• bugfixes for spectral mixture kernel

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• work around negative variances

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• NB score test: initialize alpha MLE with MoM estimator

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Commits on Jun 2, 2020

• score test: do score test before GP fitting

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• add tissue segmentation functionality

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• tissue segmentation: fix some variable names left over from testing

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Commits on Jun 4, 2020

• major refactor

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• add missing type hinting imports

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• implement reader for 10x SpaceRanger output

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• score test: fix the case where data are subset due to several

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• full sparse matrix support

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Commits on Jun 5, 2020

• score test: fix testing multiple kernels

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• simplify kernels + distance cache

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Commits on Jun 8, 2020

• tissue segmentation: fix off-by-one error

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Commits on Jun 9, 2020

• tissue segmentation: fix elbo calculation

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Commits on Jun 16, 2020

• more tissue segmentation fixes

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Commits on Jun 19, 2020

• tissue segmentation: some more elbo fixes

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Commits on Jul 8, 2020

• fix sizefactor calculation for sparse matrices

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• space ranger import: properly handle duplicate gene names

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Commits on Jul 9, 2020

• tissue segmentation: properly log about not using spatial information

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Commits on Jul 10, 2020

• tissue segmentation: tighten convergence tolerance

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Commits on Jul 14, 2020

• properly handle AnnData files with duplicate gene names in the

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• make score test work with scipy 1.5

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Commits on Sep 2, 2020

• port AEH to tensorflow with Dirichlet Process prior

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• also export SpatialPatterns class

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• aeh: clean up some imports

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Commits on Sep 7, 2020

• tissue segmentation: fix class pruning

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• tissue segmentation: adjust alpha hyperprior

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• aeh: discard unused classes after optimization

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Commits on Oct 8, 2020

• implement SVCA model

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• score test: use gpflow.default_float() consistently

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• clean up repository, modernize setup

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• black-ify

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Commits on Oct 9, 2020

• fix importing pip-installed SpatialDE

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• move kernels to _internal, set up basic sphinx-docs

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• replace old README

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Commits on Oct 12, 2020

• SVCA: allow running fit_spatial_interactions without testing first

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Commits on Oct 13, 2020

• svca.fit_spatial_interactions: properly initialize kernel

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Commits on Oct 15, 2020

• svca: better initialization

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Commits on Oct 19, 2020

• svca: use squared exponential kernel (faster)

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Commits on Oct 21, 2020

• svca: performance optimization

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Commits on Oct 22, 2020

• svca: fix test (got broken in previous commit)

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Commits on Nov 4, 2020

• fix spatially variable genes test

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Commits on Nov 5, 2020

• tissue segmentation: write the labels to the AnnData as pd.Categorical

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• Merge branch 'master' of https://github.com/ilia-kats/SpatialDE into master

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Commits on Nov 6, 2020

• svca: handle sparse matrices

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Commits on Nov 11, 2020

• aeh: save spatial patterns into adata.obs

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Commits on May 17, 2021

• when working with AnnData, allow the user to specify the layer

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Commits on Jun 28, 2021

• make setting a different default_float work for score test

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• make caching the distance matrices optional

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Commits on Aug 27, 2021

• add docstrings, adjust Sphinx config

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Commits on Aug 30, 2021

• docs: use custom template for classes

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• auto-build docs on push

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Commits on Aug 31, 2021

• update black version

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Commits on Sep 21, 2021

• test: improve speed for AnnData with lots of metadata

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Commits on Oct 1, 2021

• tissue segmentation: don't crash when no coordinates are found

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Commits on Oct 26, 2021

• workflow: use Python 3.9 for docs (no NumPy wheels for 3.10 yet)

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• docs workflow: debug

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• docs workflow: explicitly install missing NaiveDE dep

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• docs workflow: remove debug step

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• README: add docs badge

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Commits on Nov 10, 2021

• fixes for GPflow 2.1

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Commits on Jan 9, 2023

• add layer argument to GP fitting

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• some more bugfixes, black-ify

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• update pre-commit action

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• update pre-commit config

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Commits on Jan 12, 2023

• allow specifying a .obs column to use as size factor for normalization

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Commits on Jan 13, 2023

• fix SGPR model

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• fit_fast: add parameter to enable/disable sparse GPs

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Commits on Dec 20, 2024

• Add .test for Normal distribution (#1)

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• update sphinx-docs-to-gh-pages version

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