single-cell-rna-qc
scverse scRNA gold chain on .h5ad/.h5 — inspect, convert, MAD QC, optional scanpy.pp.scrublet, preprocess, Harmony/ComBat, PCA-UMAP-Leiden, Wilcoxon markers, subset, pseudobulk, pydeseq2, stable plots. Use when the user has scRNA-seq counts. Does not assign cell-type labels. rank_genes_groups is not condition DE. Do not call local doublet/ambient helpers SoupX, CellBender, or scDblFinder.
Pinned to revision aa24bdca5f23, so it is the text this page describes rather than whatever the author pushed since.
Files
- skills/single-cell-rna-qc/SKILL.md
- skills/single-cell-rna-qc/LICENSE.txt
- skills/single-cell-rna-qc/configs/gold_chain.example.json
- skills/single-cell-rna-qc/references/r_interop.md
- skills/single-cell-rna-qc/references/scverse_qc_guidelines.md
- skills/single-cell-rna-qc/scripts/_common.py
- skills/single-cell-rna-qc/scripts/ambient_rna.py
- skills/single-cell-rna-qc/scripts/doublet_detection.py
- skills/single-cell-rna-qc/scripts/qc_analysis.py
- skills/single-cell-rna-qc/scripts/qc_core.py
- skills/single-cell-rna-qc/scripts/qc_plotting.py
- skills/single-cell-rna-qc/scripts/scrna_convert.py
- skills/single-cell-rna-qc/scripts/scrna_deseq.py
- skills/single-cell-rna-qc/scripts/scrna_inspect.py
- skills/single-cell-rna-qc/scripts/scrna_integrate.py
- skills/single-cell-rna-qc/scripts/scrna_markers.py
- skills/single-cell-rna-qc/scripts/scrna_pipeline.py
- skills/single-cell-rna-qc/scripts/scrna_plot.py
- skills/single-cell-rna-qc/scripts/scrna_preprocess.py
- skills/single-cell-rna-qc/scripts/scrna_pseudobulk.py
- skills/single-cell-rna-qc/scripts/scrna_reduce_cluster.py
- skills/single-cell-rna-qc/scripts/scrna_scrublet.py
- skills/single-cell-rna-qc/scripts/scrna_subset.py
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