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Issues: OmicsML/dance

Unifying base data object
#49 opened Nov 8, 2022 by RemyLau
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Model object abstraction and refactoring
#143 opened Jan 20, 2023 by RemyLau
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Issues list

Human PDAC (ST) for Spot Deconvolution is missing true_p.csv
#455 opened Jun 28, 2024 by alyosama
Tutorial notebook is outdated
#432 opened Mar 27, 2024 by wehos
1
Errors with Installation
#431 opened Mar 27, 2024 by wehos
2
Pipeline bypass mechanism to replace *PlaceHolder transforms
#421 opened Feb 19, 2024 by RemyLau
Improve train/val/test data retrieval mech (instead of getting them individually?)
#420 opened Feb 19, 2024 by RemyLau
Random segfault when running pipeline tuning with wandb on certain machines bug Something isn't working help wanted Extra attention is needed
#407 opened Jan 30, 2024 by RemyLau
__init__.py missing from dance/metadata
#404 opened Jan 26, 2024 by cwilson51
Config support
#384 opened Dec 12, 2023 by RemyLau
Feature: sanity checks
#378 opened Dec 6, 2023 by RemyLau
Refactor multimodal dataset object to use the dance abstract dataset class
#233 opened Mar 8, 2023 by RemyLau
Fix reported imputation metrics on readme for GraphSCI and DeepImpute Priority-P0 Top priority
#227 opened Mar 3, 2023 by RemyLau
2 tasks
Use the download_unzip utility in ImputationDataset
#224 opened Feb 28, 2023 by RemyLau
Unify kwarg: seed -> random_state
#222 opened Feb 27, 2023 by RemyLau
Make utils for generating dgl or pyg graphs from processed data enhancement New feature or request
#221 opened Feb 26, 2023 by RemyLau
Add option for return_type to take a list of values aligned with the specified channels enhancement New feature or request
#216 opened Feb 26, 2023 by RemyLau
Add option to .score method to take index option, which indicates which samples we want to calculate the scores enhancement New feature or request
#214 opened Feb 23, 2023 by RemyLau
2 tasks
Fix scmm error due to zero total counts calling torch.lgamma (called by torch.distributions.NegativeBinomial)
#166 opened Jan 29, 2023 by RemyLau
Make util for auto device selection
#162 opened Jan 26, 2023 by RemyLau
Model object abstraction and refactoring Priority-P1
#143 opened Jan 20, 2023 by RemyLau
4 of 8 tasks
Add more info about key error from get_feature, e.g., what channel type
#125 opened Jan 10, 2023 by RemyLau
Exclude benchmark runs from default pytest runs, make lite-bench and full-bench test options (tox)
#122 opened Jan 9, 2023 by RemyLau
1 task
DSTG link graph add connections between real spots? question Further information is requested
#104 opened Dec 31, 2022 by RemyLau
1
Add random_state option to PCA transforms
#87 opened Dec 18, 2022 by RemyLau
Unifying base data object Priority-P0 Top priority
#49 opened Nov 8, 2022 by RemyLau
27 of 33 tasks
Some questions about general wrapper for datasets question Further information is requested
#38 opened Oct 16, 2022 by HelloWorldLTY
8
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