awesome-scRNA-analysis

integration method

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• scDREAMER

  • scDREAMER for atlas-level integration of single-cell datasets using deep generative model paired with adversarial classifier

auto annotation

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• CellSTAR

  • CellSTAR: a comprehensive resource for single-cell transcriptomic annotation

visualization

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• Doheatmap

  • Scillus: https://github.com/xmc811/Scillus

analysis pipeline

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• R

  • SingCellaR: Processing single-cell RNA-seq datasets using SingCellaR
  • Scillus: https://github.com/xmc811/Scillus

identifying tumor cells

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• • Ikarus: Identifying tumor cells at the single‑cell level using machine learning

differential analysis

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• differentially expressed genes

  • muscat: muscat detects subpopulation-specific state transitions from multi-sample multi-condition single-cell transcriptomics data

• differential abundance of celltype

  • Augur: Prioritization of cell types responsive to biological perturbations in single-cell data with Augur

pseudotime analysis

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• estimating differentiation potency

  • CCAT: Ultra-fast scalable estimation of single-cell differentiation potency from scRNA-Seq data

• pseudotime analysis

  • Cellrank: CellRank for directed single-cell fate mapping

geneset analysis

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• Gene set activity

  • SCPA: Systematic single-cell pathway analysis to characterize early T cell activation
  • irGSEA: https://github.com/chuiqin/irGSEA

cell cycle

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• cell cycle

  • tricycle: Universal prediction of cell-cycle position using transfer learning

cell align across Atlas

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• CellHint

  • Automatic cell-type harmonization and integration across Human Cell Atlas datasets

sEV analysis

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• SEVtras

  • SEVtras delineates small extracellular vesicles at droplet resolution from single-cell transcriptomes