AlexsLemonade / AlexsLemonade/rOpenScPCA
Function idea: Convert CELLxGENE AnnData to SCE
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- HTML
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Description
We have encountered a few times where we've had to convert from AnnData -> SCE, in particular when using AnnData files from CELLxGENE. One not immediately intuitive aspect of this is, after initial conversion with zellkonverter, the raw counts are stored in an altExp called `raw` as an assay named `X`, rather than as a `counts` assay in the main SCE experiment. Similarly although more intuitively, logcounts are stored in the `X` assay of the main experiment. There are also `X_` prefixes in the reduced dimensions.
We might consider writing a wrapper function to assist in performing this specific CELLxGENE AnnData -> SCE conversion that takes its particular data structure into consideration and returns an SCE object with slots labeled analogously to ScPCA data.
Contributor guide
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Research direction
No file or test is named. Start by reviewing zellkonverter's AnnData-to-SCE result and the ScPCA data structure described in the issue; done means a wrapper returns an SCE with raw counts, logcounts, and reduced dimensions labeled analogously to ScPCA data.
Written by the indexing model from the issue text.
Assessment
- Tech stack
- r
- Domain
- data
- Issue type
- Feature
- Difficulty
- 5/5
- Estimated time
- Over a week
- Activity status
- Stale
- Clarity
- Needs clarification
- Newbie friendliness
- 30/100