sculptor815/scrna-seq-workbench
Investigate biological questions with relevant scRNA-seq studies, focused analysis and traceable evidence.
Propose and review scRNA-seq cluster cell types using tissue-matched marker panels or HPA reference expression, retaining Unknown and evidence for every candidate.
Perform condition differential expression from reviewed scRNA-seq labels and raw counts using donor-level pseudobulk, explicit paired/unpaired designs and exclusions.
Inspect and filter raw scRNA-seq UMI matrices with per-sample thresholds, cell/gene exclusion ledgers and optional per-capture doublet assessment.
Investigate a biological question using public or user-provided scRNA-seq data; select relevant studies, run focused analyses and explain evidence and uncertainty.
Run default scVI or explicitly selected Harmony with cell-cycle correction; explain runtime and hardware choices, then compare clustering candidates for human selection.
Review sequencing-company scRNA-seq delivery reports (MGI DNBelab, 10x or other vendors), reconcile metrics and inventory counts/metadata before cell-level analysis.