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Genome-wide identification of E/G interactions

Introduction

Genome-wide identification of E/G interactions

Guidebooks
Guidebooks
- Introduction
- Compute summary stats of a bedpe
- Basics
  Basics
- Misc
  Misc
  - Compute correlations
Haemochromatosis
Haemochromatosis
- Introduction
- Data format
- Custom script GO
- Main results
- CHiC data
  CHiC data
- ABC data
  ABC data
BENGI
BENGI
- Introduction
- Notebooks
  Notebooks
  - Convert BENGI datasets to custom bedpe
- Summary statistics
  Summary statistics
  - Summary statistics on BENGI GM12878 benchmarks
  - (R code) Compute summary statistics over BENGI
- Evaluation of a few methods over BENGI GM12878
  Evaluation of a few methods over BENGI GM12878
  - Distance method
    Distance method
    
    Full code
    
    Results
  - DNase-expression correlation method
    DNase-expression correlation method
    
    Full code
    
    Results
  - Average rank method
    Average rank method
    
    Full code
    
    Results
- Evaluation of a few methods over Fulco et al 2019 CRISPRi-FlowFISH
  Evaluation of a few methods over Fulco et al 2019 CRISPRi-FlowFISH
  - Distance method
    Distance method
    
    Full code
    
    Results
  - DNase-expression correlation method
    DNase-expression correlation method
    
    Full code
    
    Results
  - Average rank method
    Average rank method
    
    Full code
    
    Results
ABC
ABC
- Introduction
- ABC over BENGI for GM12878, main results
- CRISPRi-FlowFISH
  CRISPRi-FlowFISH
  - Original ABC predictions over K562
  - Summary ABC over CRiFF
- Notebooks
  Notebooks
- Full codes
  Full codes
  - Test of ABC pipeline over chr22
  - ABC over GM12878 with same accessions as for BENGI
- Meld of results over chr22 vs authors' results
About
About
- Getting started
- About me

Guidebooks¶

These pages gather basic practical guidelines to work with Genotoul, and examples to use some of the scripts provided (eg Compute summary statistics of a bedpe).