├── .Rbuildignore ├── .gitignore ├── DESCRIPTION ├── LICENSE ├── NAMESPACE ├── R ├── SCassist-package.R ├── analyze_and_annotate.R ├── analyze_enrichment.R ├── analyze_pcs.R ├── analyze_quality.R ├── analyze_variable_features.R ├── recommend_k.R ├── recommend_normalization.R ├── recommend_pcs.R └── recommend_res.R ├── README.md ├── inst └── docs │ ├── LCMV-standard.html │ ├── README.md │ ├── SCassist-Tutorial-BCRUV.html │ ├── SCassist-Tutorial-LCMV.html │ ├── SCassist-prompts.md │ ├── bert-similarity.md │ ├── pub.png │ └── scassist-logo.png ├── man ├── SCassist.Rd ├── SCassist_analyze_and_annotate.Rd ├── SCassist_analyze_enrichment.Rd ├── SCassist_analyze_pcs.Rd ├── SCassist_analyze_quality.Rd ├── SCassist_analyze_variable_features.Rd ├── SCassist_recommend_k.Rd ├── SCassist_recommend_normalization.Rd ├── SCassist_recommend_pcs.Rd └── SCassist_recommend_res.Rd └── tests ├── testthat.R └── testthat ├── test-scassist_analyze_and_annotate.R ├── test-scassist_analyze_enrichment.R ├── test-scassist_analyze_pcs.R ├── test-scassist_analyze_quality.R ├── test-scassist_analyze_variable_features.R ├── test-scassist_recommend_k.R ├── test-scassist_recommend_normalization.R ├── test-scassist_recommend_pcs.R └── test-scassist_recommend_res.R /.Rbuildignore: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/NIH-NEI/SCassist/HEAD/.Rbuildignore -------------------------------------------------------------------------------- /.gitignore: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/NIH-NEI/SCassist/HEAD/.gitignore -------------------------------------------------------------------------------- /DESCRIPTION: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/NIH-NEI/SCassist/HEAD/DESCRIPTION -------------------------------------------------------------------------------- /LICENSE: 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