Single-cell data transformation documentation#193

Merged

tropnikovvl merged 75 commits intodevelopfrom

docs/sc-transformations

Apr 9, 2026

Commits on Mar 26, 2026

Single-cell data transformation draft documents

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Add different configuration reference options

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Commits on Mar 27, 2026

Refactor: minor text edit

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Fix: Remove dry_run from configuration parameters across the files

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Commits on Mar 30, 2026

Text edit

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Text edit

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Modify text describing goal of transformation

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Text edit

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Text edit

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Include reference to single cell data user guide

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Reference linking group determination

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Rename section to reference specific API endpoints

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Rephrase metadata and expression extraction description

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Modify SLP update description

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Update SLP update behaviour

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Update metadata curation description

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Update description of dry-run mode

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Update Processors controller API description

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Merge branch 'docs/sc-transformations' of https://github.com/genestack/user-docs into docs/sc-transformations

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Create attribute mapping reference

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Select desired configuration reference option, remove unwanted files

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Add gene ID - gene mapping in attribute mapping reference

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Remove supported species from gene mapping from config schema

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Update how to guide

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Update transformation reference

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Commits on Mar 31, 2026

Add quick tutorial and configurations for public datasets

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Fix configuration mapping

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Commits on Apr 1, 2026

Update links to ODM documentation

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Rename quickstart guide

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refactor: text edit

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MariaBorodaenko
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refactor: text edit

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refactor: text edit

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refactor: text edit

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refactor: text edit

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refactor: Reorganize section to preserve column names

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refactor: text edit

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refactor: text edit

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refactor: discovery mode section

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refactor: text edit

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Include reference to configuration mapping in how to

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Add reference to default values

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text edit

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rephrase columns_to_export

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rearrange secion 2.3 of transformation process reference

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rearrange explanation of qc metrics calculation

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text edit

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rephrase gene mapping section

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text edit

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text edit

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text edit

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text edit

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Reorganize New groups section

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minor text edit

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reorganize volume size and ID section

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minor text edit

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minor text edit

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minor text edit

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Simplify biosample metadata configuration section

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Add link to public configs

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Add example of group creation

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MariaBorodaenko
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Add example for linking group determination

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Add public dataset template

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Update public dataset links

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Update internal references

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Update quickstart

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Update configs

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Add table of contents and missing references

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Update quickstart guide

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Commits on Apr 6, 2026

Include modifications requested by Predrag M

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remove extended explanation from reference

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Commits on Apr 8, 2026

update about-sc

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rename notebooks

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Commits on Apr 9, 2026

minor change in notebook title

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include links to the rest of documentation

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update references

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