welcome to the documentation of spacemake

spacemake: pipeline for processing and analysing sequencing based spatial-transcriptomics data

Note

This project is under active development.

Contents

• Installation
  • Step 1: create conda environment
  • Step 2: download Dropseq-tools
  • Step 3: install spacemake
• Quick start guide
  • Initialize spacemake
  • Shared sample-variables
  • Visium quick start
    • Step 1: add a Visium sample
    • Step 2: running spacemake
  • Slide-seq quick start
    • Step 1: add a Slide-seq sample
    • Step 2: running spacemake
  • Seq-scope quick start
    • Step 1: add a Seq-scope sample
    • Step 2: running spacemake
  • scRNA-seq quick start
    • Step 1: add a single-cell RNA-seq sample
    • Step 2: running spacemake
• Initialization
  • Initializing using required arguments
  • Optional arguments
• Configuration
  • Configure species
  • Configure barcode_flavors
    • Provided barcode_flavors
    • Add a new barcode_flavor
    • Update/delete a barcode_flavor
  • Configure run_modes
    • Provided run_mode(s)
    • Add a new run_mode
    • Update/delete a run_mode
  • Configure pucks
    • Provided pucks
    • Add a new puck
• Manage projects and samples
  • Add a single sample
    • Sample parameters
    • Add a Visium/Seq-scope/Slide-seq sample
    • Add a custom spatial sample
    • Add a single-cell sample
    • Add a pre-processed count-matrix
  • Add several samples at once
  • Add samples from illumina sample-sheet
  • Listing projects
• Running spacemake
  • Main modules
  • Downsampling
• Tutorials
  • Automatic H&E alignment
    • Align H&E with Visium data
    • Align H&E with Seq-scope data
  • Manual H&E alignment
    • Before you begin
    • Step 1 - generate an expression image
    • Step 2 - load images into Fiji
    • Step 3 - select corresponding points
    • Step 4 - align the images
    • Step 5 - attach the aligned image
  • Processing a custom single-cell sample
    • Step 1: install and initialize spacemake
    • Step 2: download test data
    • Step 3: add a new species
    • Step 4: add a new barcode_flavor
    • Step 5: add a new run_mode
    • Step 6: add the sample
    • Step 7: runn spacemake
    • Step 8: results
  • Longreads Integration
    • Building blocks and Signatures
    • What happens?
    • A nanopre example
    • Graphical reports
  • Single-cell data integration with novosparc
    • Reconstructing a tissue de-novo with novosparc
    • Mapping single cell data onto spatial data using novosparc
• API and Internal API
  • API
    • Spacemake class
    • H&E integration module
    • novosparc integration module
  • Internal API
    • ProjectDF
    • ConfigFile