awesome-single-cell

List of software packages (and the people developing these methods) for single-cell data analysis, including RNA-seq, ATAC-seq, etc. Contributions welcome...

Contributors

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Citation

NotebookLM Notebook

Interact with the contents of this repository through chat, audio summary/podcast, informational video, and interactive mindmap.

• https://notebooklm.google.com/notebook/ab5c5e5c-6907-4883-8918-f4868f15ff88

Package popularity

Software packages sorted by Gitub Stars.

• https://fbnrst.github.io/awesome-single-cell-stars/

Contents

• Contributors
• Citation
• NotebookLM Notebook
• Software packages
  • RNA-seq
  • Quality control
  • Gene regulatory network identification
  • Immune receptor profiling
  • Marker and differential gene expression identification
  • Cell clustering
  • Dimension reduction
  • Archetypal analysis
  • Count modelling and normalization
  • Batch-effect removal
  • Cell projection and unimodal integration
  • Simulation
  • Pseudotime and trajectory inference
  • Cell type identification and classification
  • Malignant cell identification
  • Doublet Identification
  • Cell subsampling
  • Feature (Gene) imputation
  • Copy number analysis
  • Variant calling
  • Epigenomics
  • Multi-assay data integration
  • Rare cell detection
  • Cellular interactions/communication
  • Single cell large model
  • Other applications
  • Spatial transcriptomics
• Image-based profiling
• Tutorials and workflows
• Web portals, apps, and databases
  • Web portals and databases
  • Interactive visualization and analysis
• Journal articles of general interest
  • Paper collections
  • Big data approach overview
  • Experimental design
  • Methods comparisons
• Similar lists and collections
• People
  • Female
  • Male

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