spacemake
0.8.0
Installation
Quick start guide
Initialization
Configuration
Manage projects and samples
Running spacemake
Tutorials
Automatic H&E alignment
Manual H&E alignment
Processing a custom single-cell sample
Longreads Integration
Single-cell data integration with novosparc
Troubleshooting
API and Internal API
spacemake
Tutorials
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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
Library overview plot
Oligo alignment quality plot
Histograms
Single-cell data integration with novosparc
Reconstructing a tissue de-novo with novosparc
Mapping single cell data onto spatial data using novosparc