If you are filing this issue based on a specific GitHub Discussion, please link to the relevant Discussion.
292
Describe the goals of the changes to the analysis module.
We would like to be able to obtain clusters for all samples in the Ewing project SCPCP000015. We can then use these clusters to:
Refine the tumor and normal cell type annotations obtained using SingleR
Assign tumor cell states to sub-clusters of tumor cells (EWS-FLI1 high/low, MSC-like, proliferating phenotypes)
What will your pull request contain?
This PR should contain a template notebook that can be used to perform Jaccard, Louvain clustering across a range of nearest neighbors parameters. (See #683 for a reference). The notebook should then plot specific clustering metrics that can help us identify the most "optimal" clusters for each sample. These metrics include silhouette width, cluster purity, and cluster stability. We may also want to include plots that compare SingleR assignments to clusters.
We should also pull out many of the functions that are used in #683 into their own utils script.
Will you require additional software beyond what is already in the analysis module?
No
Will you require different computational resources beyond what the analysis module already uses?
No
If known, when do you expect to file the pull request?
If you are filing this issue based on a specific GitHub Discussion, please link to the relevant Discussion.
292
Describe the goals of the changes to the analysis module.
We would like to be able to obtain clusters for all samples in the Ewing project SCPCP000015. We can then use these clusters to:
SingleRWhat will your pull request contain?
This PR should contain a template notebook that can be used to perform Jaccard, Louvain clustering across a range of nearest neighbors parameters. (See #683 for a reference). The notebook should then plot specific clustering metrics that can help us identify the most "optimal" clusters for each sample. These metrics include silhouette width, cluster purity, and cluster stability. We may also want to include plots that compare SingleR assignments to clusters.
We should also pull out many of the functions that are used in #683 into their own
utilsscript.Will you require additional software beyond what is already in the analysis module?
No
Will you require different computational resources beyond what the analysis module already uses?
No
If known, when do you expect to file the pull request?
No response