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Usage
Getting started
📦 Installation
🚀 Quickstart
🔧 Configure Your Workflow
▶️ Call the pipeline
Configuration
⚙️ Advanced configuration
🛠️ Troubleshooting
📥 Input file mapping principles
Modules
Data preparation
Data loading
Preprocessing
Label Harmonisation
Cell Type Prediction
Doublet Detection
Quality Control
Batch Analysis
Integration
Batch Integration
Metrics
Downstream analysis
Clustering
Marker Genes
Label transfer
Majority Voting
Reference Mapping
Helper modules
Relabel Module
Filter
Subset data
Split Data
Merge
Collect
Uncollect
Tutorials
Data exploration and semi-automated quality control
Quantify batch effect
Integration pipeline
Metrics
Iterative clustering
Harmonizing cell type labels with CellHint
.rst
.pdf
Integration
Integration
#
Batch Integration
Metrics
Contributing to the module