openproblems-v2
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openproblems-bio
Formalizing and benchmarking open problems in single-cell genomics
- [ ] Create API files - [ ] Create dataset (there is no common dataset with the right gold standard features) - [ ] Create process_dataset component - [...
The SCOT method has been updated in the original github repo [rsinghlab/SCOT](https://github.com/rsinghlab/SCOT). Issues with the repo are: * requirements.txt needs to be update with scikit-learn * not a python package...
update config from scot method. Change the github package from `openproblems/SCOT` to `atong01/SCOT` when the PR atong01/SCOT#3 is merged.
**Describe the bug** The seurat_transfer method gives an error when trying to create a seurat object from anndata: ``` Error in validityMethod(as(object, superClass)) : object 'Csparse_validate' not found ``` **To...
https://openproblems.bio/documentation/create_task/design_api.html is a very difficult set of instructions to follow. Since most of this is common to all tasks (as shown in [Figure 1](https://openproblems.bio/documentation/create_task/design_api.html#fig-task-workflow)), could we generate templates of these...
If I just ran `viash test` and it failed on `test_generic_test/test_executable`, I don't want to have to wait for it to rebuild the image (from cache, yes, but still takes...
In the provided `resources_test` data, `adata.X` is None. This seems unintuitive to me.
Many academic collaborators don't have root access and therefore can't run docker. Since viash containerises everything, openproblems becomes entirely unusable if you can't run docker.
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Formalizing and benchmarking open problems in single-cell genomics