Single cell analysis

This repository serves as a review of single cell analysis methods. It borrows heavily from tutorials made available by scverse.

• Data structures review
  • Utility functions
    • Initializing AnnData
  • Subsetting AnnData
    • Adding aligned metadata
  • Observation/Variable level
  • Subsetting using metadata
    • Observation/variable-level matrices
    • Unstructured metadata
    • Layers
    • Conversion to DataFrames
    • Writing the results to disk
    • Wrapping up the introduction
    • Views and copies
    • Partial reading of large data
• Analysis review
  • Overview
  • Setup
    • Import libraries
    • Setup plotting
    • Utility functions
    • Set output folder for session
  • Import data
    • Data download
    • Data load
    • Data properties
  • Doublet removal
    • Filter transcripts by minimum number of cells with non-zero counts
    • Select highly variable genes
    • Doublet removal
    • Save/load checkpoint
    • Reload data and filter doublets
  • Preprocessing
    • Filter mitochondrial transcripts
    • Filter ribosomal transcripts
    • Calculate QC metrics
    • Filter genes by counts
    • Filter cells by number of genes
    • Review and filter QC outliers
    • Save/load checkpoint
  • Normalization
  • Clustering
    • Estimate expression variability
    • Filter highly variable genes
    • Principle components analysis
      • Regression and rescaling
      • Perform PCA
    • Clustering
    • Save/load checkpoint
  • Sample integration
    • Batch processing
    • Filter genes
    • Normalize
    • Cluster
    • Save/load checkpoint
  • Marker identification
• Velocity review
  • Setup
    • Import libraries
    • Setup plotting
    • Utility functions
  • Load data
    • Load AnnData object
    • Detailed view of adata
    • Show spliced/unspliced
  • Preprocess the Data
  • Compute RNA velocity
    • Estimate RNA velocity
    • Project the velocities
    • Interpret the velocities
  • Postprocessing
    • Identify important genes
    • Velocities in cycling progenitors
    • Speed and coherence
    • Velocity graph and pseudotime
    • PAGA velocity graph
• Plotting setup
  • Show available fonts
  • Add latin modern fonts
  • Set matplotlib to use Latin Modern fonts
  • Check rcParams after update and list fonts available to matplotlib
  • Create a test plot
• References