flowchart LR
A[Raw FASTQ] --> B[Cell Ranger]
B --> C[QC & Filtering]
C --> D[Normalization]
D --> E[Integration]
E --> F[Clustering]
F --> G[Annotation]
style A fill:#e74c3c,color:white
style B fill:#f39c12,color:white
style C fill:#3498db,color:white
style D fill:#9b59b6,color:white
style E fill:#1abc9c,color:white
style F fill:#27ae60,color:white
style G fill:#2c3e50,color:white
Single-cell RNA-seq Pipeline
Comprehensive analysis of single-cell transcriptomics data
Overview
This pipeline covers the analysis of single-cell RNA-sequencing data from raw reads to cell type annotation and downstream analysis.
Pipeline Steps
1. Cell Ranger Processing Read More →
Demultiplexing, alignment, and UMI counting with Cell Ranger.
2. Ambient RNA Correction Read More →
Removing ambient RNA contamination using CellBender.
3. Data processing and Integration Read More →
Normalization, identification of highly variable genes, and data integration.
4. Copy Number Variation Inference Read More →
For Tumor samples, infer copy number variations using Numbat.