Ecosyste.ms: Issues

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GitHub / OmicsML/dance issues and pull requests

#264 - build(deps): bump statsmodels from 0.13.5 to 0.14.0

Pull Request - State: closed - Opened by dependabot[bot] over 1 year ago
Labels: dependencies

#263 - build(deps): bump requests from 2.28.2 to 2.30.0

Pull Request - State: closed - Opened by dependabot[bot] over 1 year ago - 1 comment
Labels: dependencies

#262 - build(deps-dev): bump tox from 4.4.12 to 4.5.1

Pull Request - State: closed - Opened by dependabot[bot] almost 2 years ago - 1 comment
Labels: dependencies

#261 - build(deps): bump requests from 2.28.2 to 2.29.0

Pull Request - State: closed - Opened by dependabot[bot] almost 2 years ago - 1 comment
Labels: dependencies

#260 - build(deps): bump pandas from 2.0.0 to 2.0.1

Pull Request - State: closed - Opened by dependabot[bot] almost 2 years ago - 1 comment
Labels: dependencies

#259 - build(deps): bump torch-geometric from 2.3.0 to 2.3.1

Pull Request - State: closed - Opened by dependabot[bot] almost 2 years ago - 2 comments
Labels: dependencies

#258 - pip install pydance

Issue - State: closed - Opened by schwartznicholas almost 2 years ago - 1 comment
Labels: installation

#257 - Running scmogcn.py example - fatal error

Issue - State: closed - Opened by valtado1 almost 2 years ago - 1 comment

#256 - Where can I find documenation?

Issue - State: closed - Opened by ajbenz18 almost 2 years ago - 1 comment

#255 - doc: update installation instructions on readme

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

#254 - build(deps): bump scikit-misc from 0.1.4 to 0.2.0

Pull Request - State: closed - Opened by dependabot[bot] almost 2 years ago
Labels: dependencies

#253 - build(deps-dev): bump pytest from 7.2.2 to 7.3.1

Pull Request - State: closed - Opened by dependabot[bot] almost 2 years ago
Labels: dependencies

#252 - build(deps-dev): bump tox from 4.4.11 to 4.4.12

Pull Request - State: closed - Opened by dependabot[bot] almost 2 years ago
Labels: dependencies

#251 - [pre-commit.ci] pre-commit autoupdate

Pull Request - State: closed - Opened by pre-commit-ci[bot] almost 2 years ago

#250 - build(deps): bump networkx from 3.0 to 3.1

Pull Request - State: closed - Opened by dependabot[bot] almost 2 years ago
Labels: dependencies

#249 - build(deps-dev): bump tox from 4.4.8 to 4.4.11

Pull Request - State: closed - Opened by dependabot[bot] almost 2 years ago
Labels: dependencies

#248 - build(deps-dev): bump pre-commit from 3.2.1 to 3.2.2

Pull Request - State: closed - Opened by dependabot[bot] almost 2 years ago
Labels: dependencies

#247 - build(deps): bump pandas from 1.5.3 to 2.0.0

Pull Request - State: closed - Opened by dependabot[bot] almost 2 years ago
Labels: dependencies

#246 - build(deps): bump mudata from 0.2.1 to 0.2.2

Pull Request - State: closed - Opened by dependabot[bot] almost 2 years ago
Labels: dependencies

#245 - error about running dataset(openproblems_bmmc_cite_phase2 ) with scMoGCN

Issue - State: closed - Opened by yuxiaokang-source almost 2 years ago - 1 comment

#244 - update installation script (pytorch 2.0, pyg2.3, dgl1.0)

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

#243 - build(deps-dev): bump tox from 4.4.7 to 4.4.8

Pull Request - State: closed - Opened by dependabot[bot] almost 2 years ago
Labels: dependencies

#242 - [pre-commit.ci] pre-commit autoupdate

Pull Request - State: closed - Opened by pre-commit-ci[bot] almost 2 years ago

#241 - build(deps-dev): bump pre-commit from 3.2.0 to 3.2.1

Pull Request - State: closed - Opened by dependabot[bot] almost 2 years ago
Labels: dependencies

#240 - fix: divid x_norm by mean instead of sum as in the original implement…

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

#239 - Fix minor inconsistency at param init for CARD

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

#238 - build(deps-dev): bump pre-commit from 3.1.1 to 3.2.0

Pull Request - State: closed - Opened by dependabot[bot] almost 2 years ago - 1 comment
Labels: dependencies

#237 - build(deps-dev): bump pytest-xdist from 3.2.0 to 3.2.1

Pull Request - State: closed - Opened by dependabot[bot] almost 2 years ago - 1 comment
Labels: dependencies

#236 - build(deps-dev): bump tox from 4.4.6 to 4.4.7

Pull Request - State: closed - Opened by dependabot[bot] almost 2 years ago - 1 comment
Labels: dependencies

#235 - build(deps): bump openpyxl from 3.1.1 to 3.1.2

Pull Request - State: closed - Opened by dependabot[bot] almost 2 years ago - 1 comment
Labels: dependencies

#234 - build(deps): bump scikit-learn from 1.2.1 to 1.2.2

Pull Request - State: closed - Opened by dependabot[bot] almost 2 years ago - 1 comment
Labels: dependencies

#232 - build(deps-dev): bump pytest from 7.2.1 to 7.2.2

Pull Request - State: closed - Opened by dependabot[bot] almost 2 years ago - 1 comment
Labels: dependencies

#231 - build(deps): bump scanpy from 1.9.2 to 1.9.3

Pull Request - State: closed - Opened by dependabot[bot] almost 2 years ago - 1 comment
Labels: dependencies

#230 - build(deps): bump tqdm from 4.64.1 to 4.65.0

Pull Request - State: closed - Opened by dependabot[bot] almost 2 years ago - 1 comment
Labels: dependencies

#229 - build(deps-dev): bump pre-commit from 3.1.0 to 3.1.1

Pull Request - State: closed - Opened by dependabot[bot] almost 2 years ago - 1 comment
Labels: dependencies

#228 - refactor: multiomics modules

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

#227 - Fix reported imputation metrics on readme for `GraphSCI` and `DeepImpute`

Issue - State: open - Opened by RemyLau almost 2 years ago
Labels: Priority-P0

#226 - fix: load FilterGenesMarker transform

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

#225 - replace scGNN with scGNN2.0

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

#224 - Use the `download_unzip` utility in `ImputationDataset`

Issue - State: open - Opened by RemyLau almost 2 years ago

#223 - refactor: `DeepImput` & `GraphSCI` imputation modules (dataset + transform)

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

#222 - Unify kwarg: `seed` -> `random_state`

Issue - State: open - Opened by RemyLau almost 2 years ago

#221 - Make utils for generating `dgl` or `pyg` graphs from processed data

Issue - State: open - Opened by RemyLau almost 2 years ago
Labels: enhancement

#220 - build(deps): bump opencv-python from 4.7.0.68 to 4.7.0.72

Pull Request - State: closed - Opened by dependabot[bot] almost 2 years ago - 1 comment
Labels: dependencies

#219 - build(deps-dev): bump tox from 4.4.5 to 4.4.6

Pull Request - State: closed - Opened by dependabot[bot] almost 2 years ago - 1 comment
Labels: dependencies

#218 - build(deps-dev): bump pre-commit from 3.0.4 to 3.1.0

Pull Request - State: closed - Opened by dependabot[bot] almost 2 years ago - 1 comment
Labels: dependencies

#217 - fix: remove unused; do not set mutable default kwargs

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

#216 - Add option for `return_type` to take a list of values aligned with the specified channels

Issue - State: open - Opened by RemyLau almost 2 years ago
Labels: enhancement

#215 - refactor: adapt cell type deconvolution modules to ``BaseRegressionMethod``

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

#213 - refactor: update card to use dance transformations

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

#212 - refactor: udpate dstg example script to use dance transforms

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

#211 - refactor: create preprocessing pipelines for Spotlight and SpatialDecon

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

#210 - refactor: adapt ``CellTypeDeconvoDataset`` to ``BaseDataset`` class

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

#209 - feat: implement append method to dance data object

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

#208 - Bump scipy from 1.10.0 to 1.10.1

Pull Request - State: closed - Opened by dependabot[bot] almost 2 years ago - 1 comment
Labels: dependencies

#207 - feat: add option to initialize splits from dict

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

#206 - feat: implement FilterGenesCommon gene selection transformation

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

#205 - fix: update test bench cli arguments for clustering examples

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

#204 - refactor: adapt ``Stagate`` to ``BasePretrain`` class; improve consistency

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

#203 - use logger; minor edits

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

#202 - refactor: adapt ``ClusteringDataset`` to BaseDataset

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

#201 - format: unify clustering example scripts formats

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

#200 - refactor: adapt scdcc to ``BaseClusteringMethod`` and ``TorchNNPretrain``

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

#197 - Bump pytest-subtests from 0.9.0 to 0.10.0

Pull Request - State: closed - Opened by dependabot[bot] almost 2 years ago - 1 comment
Labels: dependencies

#196 - Bump scanpy from 1.9.1 to 1.9.2

Pull Request - State: closed - Opened by dependabot[bot] almost 2 years ago - 1 comment
Labels: dependencies

#195 - refactor: adapt graph-sc to ``BaseClusteringMethod`` object

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

#194 - fix: set edge weights for normalized adjacency in sctag

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

#193 - refactor: `sctag` model -> `BaseClusteringMethod`

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

#191 - refactor: use dance transform in ``graphsc`` example scripts

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

#190 - format: minor format fixes for multi modality modules and example scripts

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

#189 - refactor: use dance transformations in clustering example scripts

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

#188 - Reformat data for multimodality

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

#187 - reformat data for multimodality

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

#186 - fix clustering example scripts code styles

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

#185 - [pre-commit.ci] pre-commit autoupdate

Pull Request - State: closed - Opened by pre-commit-ci[bot] almost 2 years ago

#184 - fix: torch installation and update dgl channel

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

#183 - Bump tox from 4.4.2 to 4.4.5

Pull Request - State: closed - Opened by dependabot[bot] almost 2 years ago - 2 comments
Labels: dependencies

#182 - Bump pytest-xdist from 3.1.0 to 3.2.0

Pull Request - State: closed - Opened by dependabot[bot] almost 2 years ago - 2 comments
Labels: dependencies

#181 - remove unused libraries

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

#180 - Bump tox from 4.4.2 to 4.4.4

Pull Request - State: closed - Opened by dependabot[bot] almost 2 years ago - 1 comment
Labels: dependencies

#179 - Bump pre-commit from 3.0.1 to 3.0.4

Pull Request - State: closed - Opened by dependabot[bot] almost 2 years ago
Labels: dependencies

#178 - refactoring of code

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

#177 - updating parameter initialization

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

#176 - updating test_data parameters

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

#175 - Add support for containerizing using, e.g., Singularity and Docker

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

#174 - Create tutorial notebook for wrapping ``AnnData`` (or ``MuData``) objects into dance ``Data`` object

Issue - State: closed - Opened by RemyLau about 2 years ago - 1 comment
Labels: Priority-P0

#173 - Bump pre-commit from 3.0.1 to 3.0.2

Pull Request - State: closed - Opened by dependabot[bot] about 2 years ago - 1 comment
Labels: dependencies

#172 - Bump tox from 4.4.2 to 4.4.3

Pull Request - State: closed - Opened by dependabot[bot] about 2 years ago - 1 comment
Labels: dependencies

#171 - Bump openpyxl from 3.0.10 to 3.1.0

Pull Request - State: closed - Opened by dependabot[bot] about 2 years ago - 1 comment
Labels: dependencies

#170 - update spatial domain modules to inherit from ``BaseClusteringMethod``

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

#168 - [pre-commit.ci] pre-commit autoupdate

Pull Request - State: closed - Opened by pre-commit-ci[bot] about 2 years ago

#167 - Bump pre-commit from 3.0.0 to 3.0.1

Pull Request - State: closed - Opened by dependabot[bot] about 2 years ago
Labels: dependencies

#143 - Model object abstraction and refactoring

Issue - State: open - Opened by RemyLau about 2 years ago
Labels: Priority-P1

#49 - Unifying base data object

Issue - State: open - Opened by RemyLau about 2 years ago
Labels: Priority-P0

#38 - Some questions about general wrapper for datasets

Issue - State: open - Opened by HelloWorldLTY over 2 years ago - 8 comments
Labels: question