AlexsLemonade / AlexsLemonade/rOpenScPCA

Function idea: Convert CELLxGENE AnnData to SCE

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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.

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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

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