├── .editorconfig ├── .gitattributes ├── .github └── workflows │ └── main.yml ├── .gitignore ├── .test ├── cells.tsv ├── config.yaml ├── counts.tsv └── resources │ └── markers.tsv ├── LICENSE ├── README.md ├── Snakefile ├── cells.tsv ├── config.yaml ├── envs ├── cellassign.yaml ├── edger.yaml ├── eval.yaml └── heatmap.yaml ├── report ├── 50-highest-genes.rst ├── avg-counts.rst ├── cellassign.rst ├── celltype-expressions.rst ├── celltype-markers.rst ├── celltype-tsne.rst ├── cycle-scores.rst ├── diffexp-bcv.rst ├── diffexp-disp.rst ├── diffexp-md.rst ├── diffexp-table.rst ├── explained-variance.rst ├── expressed-genes.rst ├── filtering.rst ├── gene-tsne.rst ├── gene-vs-gene-plot.rst ├── goi.rst ├── hvg-clusters.rst ├── hvg-corr-heatmap.rst ├── hvg-corr-pca.rst ├── hvg-corr-tsne.rst ├── hvg-correlations.rst ├── hvg-expr-dists.rst ├── hvg.rst ├── library-size.rst ├── markers.rst ├── mean-vs-variance.rst ├── mito-proportion.rst ├── size-factors.rst ├── spike-proportion.rst └── workflow.rst ├── resources └── markers.tsv ├── rules ├── cell-cycle.smk ├── cell-type.smk ├── common.smk ├── counts.smk ├── diffexp.smk ├── filtration.smk ├── normalization.smk ├── qc.smk └── variance.smk ├── schemas ├── cells.schema.yaml └── config.schema.yaml └── scripts ├── batch-effect-removal.R ├── cell-cycle-scores.R ├── cell-cycle.R ├── cellassign.R ├── celltype-tsne.R ├── common.R ├── diffexp.R ├── explained-variance.R ├── filter-cells.R ├── filter-genes.R ├── gene-tsne.R ├── hvg-correlation.R ├── hvg-pca.R ├── hvg-tsne.R ├── hvg.R ├── load-counts.R ├── normalize.R ├── plot-cellassign.R ├── plot-differential-expression.R ├── plot-gene-expression.R ├── plot-gene-gene-expression.R ├── qc.R └── size-factors.R /.editorconfig: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/snakemake-workflows/single-cell-rna-seq/HEAD/.editorconfig -------------------------------------------------------------------------------- /.gitattributes: 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