15 days ago
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Restructure code/analysis/ into scRNA-seq_code/ and Bulk-code/ subdirectories
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Delete code/analysis/md
16 days ago
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Fix file encoding of the previous documentation commit
Restore plain UTF-8 file contents for the translated code comments and dataset notes. -
Translate code comments to English and align dataset notes
English documentation for the analysis and validation scripts, and consistent dataset notes across the release.
22 days ago
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Provide six-panel downstream QC figures, source tables and reproducible plotting code
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Update TCGA survival inputs, Cox results, diagnostics and reproducible workflow
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Translate annotation comparison comments and usage notes into English
23 days ago
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Restore Harmony parameter context and source clustering seeds
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Complete single-cell parameter records and group single-cell and bulk settings by function
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Organize validation code by QC, annotation comparison, markers and figures
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Update Figure 2 with five-cohort annotation concordance and reproducible scripts
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Exclude model-derived cohorts and align collection statistics and figures
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Clarify expression units, source provenance and data use terms
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Add CSV expression and metadata download archives
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Reconcile submission source tables and document historical comparison limits
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Add independent SingleR and scType annotations while retaining source labels
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Correct source metadata and document current QC fields and code usage
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Support current single-cell QC formats in figure data extraction
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Complete annotation coverage and matrix integrity summaries for the updated release
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Align provenance and validation documentation with updated collection
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Exclude mouse transplant accession and update human collection statistics
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Add curated single-cell comparative analyses and recorded parameters
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Clarify historical software defaults and parameter documentation
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Provide technical validation code and annotation comparison evidence
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Simplify code directory and standardize analysis script names
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Include complete independent analysis code snapshot
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Document source limits and provide metadata-aware reading utilities
