Week 15/08/2024

[olivierlabayle]

Thesis Writing:

• [x] Thesis title
• [x] Submit intention to submit
• [ ] The not so close closest estimands
• [ ] TarGene discussion
• [ ] Describe available workflows
• [x] Background: Causal Inference
• [x] Discuss differences betwee=n Genotyping, Imputation and Sequencing
• [x] Background: From Association Studies Back to Causal Mechanisms
• [x] Linear Model Foundation and inference
• [x] Mixed Linear Model and variations
• [x] Speak about why front door not going to help
• [x] KnockOff
• [ ] Background: OneStep and TMLE

Simulation Study:

• [ ] Migrate the reusable code to Simulations.jl and further test
• [x] Migrate the run setup and plots to another repo within EdBiomedical
• [ ] High dimensional variance should include the idnentity matrix
• [ ] Null Simulation Analysis
  • [ ] Run (Resume once realistic is done)
  • [ ] Check if all linked variants are in HLA region
  • [ ] ...
• [ ] Realistic Simulation Analysis
  • [ ] Analyse when run finished and ad to thesis

DB:

• [ ] Review PR

VDR paper:

• [ ] Setup Joint Repo for Kelsey and I
• [ ] Write joint config
• [ ] Rerun both
• [ ] Analyse

TarGene CleanUp:

• [ ] https://github.com/TARGENE/targene-pipeline/issues/179#issue-2303134191
• [x] Cleanup APIs TargeneCore
• [ ] Update and Add more native estimator configs
• [ ] MultiArch docker images across org?
• [ ] executable TMLE CLI
• [ ] estimator configs by name at targene level
• [ ] Remove the STUDY_DESIGN parameter and infer the mode(s) from the yaml/jls file(s)?
• [ ] Release Targene packages in julia registry for better deps management
• [ ] Add a Quick Start section
• [ ] Add a "famous" simulation to TMLE.jl docs?