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Releases: OmicsML/dance

DNACE 1.0.1: Bug fixes & new datasets

04 Dec 00:01
@RemyLau RemyLau
v1.0.1
f3701f0
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DNACE 1.0.1: Bug fixes & new datasets Latest
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What's Changed

Dependencies

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Full Changelog: v1.0.0...v1.0.1

Contributors

szhorvat, dependabot, and 3 other contributors
Assets 2

DANCE v1.0.0 release

29 Jun 17:00
@RemyLau RemyLau
v1.0.0
1be67e9
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DANCE v1.0.0 release

What's Changed

  • improve scmogcn sampling by @RemyLau in #28
  • fix: scmogcn device by @RemyLau in #30
  • create cell feature function (updated version of gen_batch_feature) by @RemyLau in #39
  • fix copyright notices by @RemyLau in #40
  • refactor data object and update svm by @RemyLau in #56
  • refactor label adata processing to increase compatibility with user defined datasets by @RemyLau in #57
  • matrix normalization utility by @RemyLau in #58
  • refactor cell feat transform by @RemyLau in #59
  • fix tox testing environment: install dev extra dependencies by @RemyLau in #60
  • add shortcut properties for train/val/test index by @RemyLau in #62
  • update actinn example script with new data object by @RemyLau in #63
  • update data API by @RemyLau in #64
  • update celltypist example script to use dance data object by @RemyLau in #72
  • update scDeepSort example script to use dance data object by @RemyLau in #75
  • update singlecellnet to use dance data object by @RemyLau in #77
  • fix: update data split index test by @RemyLau in #78
  • update data object to support multiple feature by @RemyLau in #79
  • support more channel types in data object by @RemyLau in #80
  • fix: slice both columns and rows for pairwise features by @RemyLau in #81
  • refactor graph transforms and rename Gene -> Feature by @RemyLau in #82
  • fix: add missing mudata dependency by @RemyLau in #84
  • refactor spagcn graph construct; use dance data object in the example spagcn script by @RemyLau in #83
  • add more complex support to label channels; replace layer option with channel_type by @RemyLau in #88
  • update babel example script to use dance data object by @RemyLau in #89
  • update card cell-type deconvolution example script using dance data object by @RemyLau in #93
  • update spatialdeconv to use dance data object by @RemyLau in #94
  • Update clustering examples to use data object by @WenzhuoTang in #95
  • fix action dependency by @RemyLau in #96
  • remove deprecated args by @RemyLau in #102
  • update dstg example script to use dance data, refactor dstg graph construct by @RemyLau in #103
  • implement AnnDataTransform interface by @RemyLau in #106
  • update spotlight example script to use dance data object by @RemyLau in #107
  • fix typos in the code-base that remy has worked on by @RemyLau in #111
  • Create CODE_OF_CONDUCT.md by @RemyLau in #112
  • fix spotlight score function arg types by @RemyLau in #113
  • use data load in dstg and update nx api call by @RemyLau in #119
  • clean up spatial deconv datasets; improve ct_select alignment by @RemyLau in #120
  • add contribution guidelines by @RemyLau in #121
  • add support for single column feature retrieval from data object by @RemyLau in #123
  • update louvain example script to use dance dataobject by @RemyLau in #124
  • update stlearn example script to use dance data object by @RemyLau in #126
  • update stagate example script to use dance data object by @RemyLau in #127
  • fix typo in readme with other minor edits by @RemyLau in #128
  • pydance -> dance when applicable for consistency by @RemyLau in #129
  • unify cell-type annotation dataloader and example scripts format by @RemyLau in #137
  • remove deprecated functions and improve url dict format by @RemyLau in #138
  • remove unused params and transformations in celltypist by @RemyLau in #139
  • add options to return predicted labels; improve log msg by @RemyLau in #140
  • update checkout and setup-python actions versions by @RemyLau in #141
  • add majority voting parser option to celltypist example; improve log msg by @RemyLau in #142
  • format and docstring edits for spatial modules by @RemyLau in #144
  • Aditya - Reproduction Info Updated by @adiark in #145
  • implement BaseDataset object with caching option by @RemyLau in #151
  • Aditya - Changing cell node initializing value from Nan to data index by @adiark in #146
  • refactor scn preprocessing by @RemyLau in #152
  • update readme by @RemyLau in #153
  • upload scn_feature.py by @RemyLau in #154
  • fix action and tests by @RemyLau in #155
  • fix doc deps and create api pages by @RemyLau in #156
  • format docstring, use auto doc typehints by @RemyLau in #160
  • update twitter badge by @RemyLau in #161
  • create BaseMethod abstraction and refactor models by @RemyLau in #163
  • upload missing file by @RemyLau in #164
  • refactor preprocessing pipelines for spatial_domain tasks by @RemyLau in #165
  • install requirements automatically from install.sh by @RemyLau in #169
  • remove unused libraries by @RemyLau in #181
  • fix: torch installation and update dgl channel by @RemyLau in #184
  • fix clustering example scripts code styles by @RemyLau in #186
  • Reformat data for multimodality by @wehos in #188
  • refactor: use dance transformations in clustering example scripts by @RemyLau in #189
  • format: minor format fixes for multi modality modules and example scripts by @RemyLau in #190
  • refactor: use dance transform in graphsc example scripts by @RemyLau in #191
  • refactor: wrap method specific composed preprocessing pipelines for clustering examples by @RemyLau in #192
  • refactor: sctag model -> BaseClusteringMethod by @RemyLau in #193
  • fix: set edge weights for normalized adjacency in sctag by @RemyLau in #194
  • refactor: adapt graph-sc to BaseClusteringMethod object by @RemyLau in #195
  • refactor: adapt scdsc to BaseClusteringMethod class; create BasePretrain mixin by @RemyLau in #198
  • refactor: adapt scdeepcluster to BaseClusteringMethod and TorchNNPretrain by @RemyLau in #199
  • refactor: adapt scdcc to BaseClusteringMethod and TorchNNPretrain by @RemyLau in #200
  • format: unify clustering example scripts formats by @RemyLau in #201
  • refactor: adapt ClusteringDataset to BaseDataset by @RemyLau in #202
  • update spatial domain modules to inherit from BaseClusteringMethod by @RemyLau in #170
  • use logger; minor edits by @RemyLau in #203
  • refactor: adapt Stagate to BasePretrain class; improve consistency by @RemyLau in #204
  • feat: implement FilterGenesCommon gene selection transformation by @RemyLau in #206
  • feat: add option to initialize splits from dict by @RemyLau in #207
  • fix: update test bench cli arguments for clustering examples by @RemyLau in #205
  • feat: implement append method to dance data object by @RemyLau in #209
  • refactor: adapt CellTypeDeconvoDataset to BaseDataset class by @RemyLau in #210
  • refactor: create preprocessing pipelines for Spotlight and SpatialDecon by @RemyLau in #211
  • refactor: udpate dstg example script to use dance transforms by @RemyLau in https://github.com/OmicsML/d...
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Contributors

wehos, RemyLau, and 3 other contributors
Assets 2

v1.0.0rc0

21 Aug 01:02
@RemyLau RemyLau
v1.0.0rc0
b1f3090
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v1.0.0rc0 Pre-release
Pre-release 
Add usage notes to README (#10)
Assets 2