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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

Commits on Jan 15, 2020

• fix s2_t_hat calculation

  ilia-kats

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  1db4060

Commits on Jan 29, 2020

• First port of SpatialDE to gpflow + tensorflow

  Show description for 1727ab2
  ilia-kats

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  1727ab2

• remove apparently unused file

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  c125580

Commits on Feb 11, 2020

• fix s2_t_hat calculation

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  ef72229

• remove apparently unused file

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  2f0737b

Commits on Mar 5, 2020

• add option to use score test instead of LRT test

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  8a0c4f4

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

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  ded3891

Commits on Mar 17, 2020

• do not fit multiple GPs for multiple kernels

  Show description for 1e570ae
  ilia-kats

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  1e570ae

Commits on Mar 18, 2020

• enable pickling of frozen models, improve power spectrum plot

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  d8f03a4

• fix deleted function in __init__.py

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  cdec422

Commits on Mar 20, 2020

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

  Show description for 22717c6
  ilia-kats

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  22717c6

Commits on Mar 23, 2020

• full refactor

  Show description for 84cae8b
  ilia-kats

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  84cae8b

Commits on Mar 24, 2020

• minor bugfixes

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  09c441d

Commits on Mar 27, 2020

• refactor score tests in prepration for NB null model

  Show description for 781aba7
  ilia-kats

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  781aba7

Commits on Mar 30, 2020

• testing negative binomial null model

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  b09ad95

• performance: perform score test once per gene and model

  Show description for dd1d203
  ilia-kats

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  dd1d203

Commits on Mar 31, 2020

• Merge branch 'gpflow'

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  9a19a45

• fix up some merge issues

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  5a6902b

Commits on Apr 6, 2020

• fully integrate gpflow into spatialde

  Show description for db545ad
  ilia-kats

  committed
  db545ad

Commits on Apr 8, 2020

• robustify against singular matrices, some bugfixes

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  b687830

Commits on Apr 14, 2020

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

  Show description for f9d400b
  ilia-kats

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  f9d400b

• clean up obsolete functions

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  a0b3227

• setup: bump version, add gpflow dependency

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  9714c83

• remove deleted function from __init__.py

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  11ef99e

Commits on Apr 15, 2020

• increase minimum lengthscale for automatically generated kernel space

  Show description for 88cf687
  ilia-kats

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  88cf687

• bugfixes for spectral mixture kernel

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  fbd166d

• work around negative variances

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  2217ff2

• NB score test: initialize alpha MLE with MoM estimator

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  599abb4

Commits on Jun 2, 2020

• score test: do score test before GP fitting

  Show description for 8809ddf
  ilia-kats

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  8809ddf

• add tissue segmentation functionality

  Show description for 0e4b883
  ilia-kats

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  0e4b883

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

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  fd44a3c

Commits on Jun 4, 2020

• major refactor

  Show description for 62597ea
  ilia-kats

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  62597ea

• add missing type hinting imports

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  a1749f5

• implement reader for 10x SpaceRanger output

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  065ea38

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

  Show description for 0d24dec
  ilia-kats

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  0d24dec

• full sparse matrix support

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  1d32da8

Commits on Jun 5, 2020

• score test: fix testing multiple kernels

  Show description for 27bcc40
  ilia-kats

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  27bcc40

• simplify kernels + distance cache

  Show description for fd76bcd
  ilia-kats

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  fd76bcd

Commits on Jun 8, 2020

• tissue segmentation: fix off-by-one error

  Show description for ff61793
  ilia-kats

  committed
  ff61793

Commits on Jun 9, 2020

• tissue segmentation: fix elbo calculation

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  3fc4f73

Commits on Jun 16, 2020

• more tissue segmentation fixes

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  7404517

Commits on Jun 19, 2020

• tissue segmentation: some more elbo fixes

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  be9ff05

Commits on Jul 8, 2020

• fix sizefactor calculation for sparse matrices

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  28a5477

• space ranger import: properly handle duplicate gene names

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  5014f93

Commits on Jul 9, 2020

• tissue segmentation: properly log about not using spatial information

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  1694543

Commits on Jul 10, 2020

• tissue segmentation: tighten convergence tolerance

  Show description for 389cc57
  ilia-kats

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  389cc57

Commits on Jul 14, 2020

• properly handle AnnData files with duplicate gene names in the

  Show description for 8e088d3
  ilia-kats

  committed
  8e088d3

• make score test work with scipy 1.5

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  76630fe

Commits on Sep 2, 2020

• port AEH to tensorflow with Dirichlet Process prior

  Show description for b568612
  ilia-kats

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  b568612

• also export SpatialPatterns class

  ilia-kats

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  eb78e70

• aeh: clean up some imports

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  f3905b5

Commits on Sep 7, 2020

• tissue segmentation: fix class pruning

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  468360e

• tissue segmentation: adjust alpha hyperprior

  Show description for 4c44a7a
  ilia-kats

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  4c44a7a

• aeh: discard unused classes after optimization

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  8068e0a

Commits on Oct 8, 2020

• implement SVCA model

  Show description for 75898a2
  ilia-kats

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  75898a2

• score test: use gpflow.default_float() consistently

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  d2dd0bf

• clean up repository, modernize setup

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  fe9e67b

• black-ify

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  5a7472f

Commits on Oct 9, 2020

• fix importing pip-installed SpatialDE

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  f13a046

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

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  4bbe4b4

• replace old README

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  f09094d

Commits on Oct 12, 2020

• SVCA: allow running fit_spatial_interactions without testing first

  Show description for 2dd0fb2
  ilia-kats

  committed
  2dd0fb2

Commits on Oct 13, 2020

• svca.fit_spatial_interactions: properly initialize kernel

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  0d6b7c8

Commits on Oct 15, 2020

• svca: better initialization

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  262dec6

Commits on Oct 19, 2020

• svca: use squared exponential kernel (faster)

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  81a7038

Commits on Oct 21, 2020

• svca: performance optimization

  Show description for 5b93d99
  ilia-kats

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  5b93d99

Commits on Oct 22, 2020

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

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  916e0e3

Commits on Nov 4, 2020

• fix spatially variable genes test

  Show description for 8c3d7c8
  ilia-kats

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  8c3d7c8

Commits on Nov 5, 2020

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

  Show description for 6cc9e16
  ilia-kats

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  6cc9e16

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

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  f3a853f

Commits on Nov 6, 2020

• svca: handle sparse matrices

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  e93cef6

Commits on Nov 11, 2020

• aeh: save spatial patterns into adata.obs

  Show description for 3c15d79
  ilia-kats

  committed
  3c15d79

Commits on May 17, 2021

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

  ilia-kats

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  267fd68

Commits on Jun 28, 2021

• make setting a different default_float work for score test

  Show description for 714a63c
  ilia-kats

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  714a63c

• make caching the distance matrices optional

  Show description for 4da263e
  ilia-kats

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  4da263e

Commits on Aug 27, 2021

• add docstrings, adjust Sphinx config

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  ec40f5a

Commits on Aug 30, 2021

• docs: use custom template for classes

  Show description for 603fbaf
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  603fbaf

• auto-build docs on push

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  6bd6d1c

Commits on Aug 31, 2021

• update black version

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  13eddb8

Commits on Sep 21, 2021

• test: improve speed for AnnData with lots of metadata

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  f9ff81f

Commits on Oct 1, 2021

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

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  37e22ad

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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  44d5dbe

• docs workflow: explicitly install missing NaiveDE dep

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• docs workflow: remove debug step

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  bc8ee56

• README: add docs badge

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  906c5e7

Commits on Nov 10, 2021

• fixes for GPflow 2.1

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  78da0ac

Commits on Jan 9, 2023

• add layer argument to GP fitting

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  a3d5ec7

• some more bugfixes, black-ify

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  0e27c17

• update pre-commit action

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  cde7720

• update pre-commit config

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  c5aa9cd

Commits on Jan 12, 2023

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

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  42b076c

Commits on Jan 13, 2023

• fix SGPR model

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  a69ba45

• fit_fast: add parameter to enable/disable sparse GPs

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  25f96b6

Commits on Dec 20, 2024

• Add .test for Normal distribution (#1)

  Show description for 3703cef
  jykr

  authored
  3703cef

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

  ilia-kats

  authored
  6dbdb55