AlexsLemonade / AlexsLemonade/OpenScPCA-analysis

Explore use of pooled normal reference with inferCNV in solid tumors of interest

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Description

This Epic tracks work to explore if using pooled normal reference with inferCNV can improve classification of tumor vs normal cells across solid tumor projects of interest.

Noting this epic was originally opened to track work in Neuroblastoma samples from project `SCPCP000004`, but I've rethought this somewhat and have modified this epic description/name to generally track progress in the `infercnv-consensus-cell-type` module.

Contributor guide

Open the contributing guide

Research direction

Start by reviewing the infercnv-consensus-cell-type module and the original Neuroblastoma context in project SCPCP000004. Compare whether pooled normal references improve tumor-versus-normal classification across the solid tumor projects of interest; done means the exploration has a documented conclusion and supporting results.

Written by the indexing model from the issue text.

Assessment

Domain
bioinformatics
Issue type
Feature
Difficulty
5/5
Estimated time
Over a week
Activity status
Stale
Clarity
Needs clarification
Newbie friendliness
20/100

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