Clindet documentation

Contents:

• Quick Start
  • 1. Clindet
  • 2. Setup Clindet
  • 3. Use case
• DNAseq analysis
  • 1. Whole exome sequence data analysis
  • 2. Whole genome sequence data analysis
• RNAseq analysis
  • 1. ClinDet RNA-seq workflow
• Use Case
  • 1. Use case I: SNV and CNV calling from Whole exome sequencing data
  • 2. Use case II: Fusion genes detection from multiple myeloma patient RNA-seq
  • 3. Use case III: Whole genome sequencing of COLO829 cell line
  • 4. Use case IV: Quantifying​​ the contributions of DNA repair defective gene mutations to mutational signatures（C.elegans）
  • 5. Use case V: Switching to different genome version (e.g. hg38)
• A Gym for Clinical NGS Data Analysis Workflows
  • 1. Clinical Omics Benchmark Datasets
  • 2. Benchmark
• snakemake/clindet: Citations
  • snakemake
  • Pipeline tools
  • Software packaging/containerisation tools

Indices and tables

• Index

• Module Index

• Search Page