PhD

Credible Sets (1st Year PhD)

2018:

• Intro1

• Intro2

• 16 Oct 2018

• 26 Oct 2018

• 1 Nov 2018

• 13 Nov 2018

• 20 Nov 2018

• 30 Nov 2018

• 7 Dec 2018

• 8 Dec 2018

2019:

• Frequentist vrs Bayesian genetic association testing

• Deriving PPs

• 16 Jan 2019

• 23 Jan 2019

• 12 Feb 2019

• 20 Feb 2019

• 27 Feb 2019

• 6 March 2019

• 13 March 2019

• 20 March 2019

• 27 March 2019

• 3 April 2019

• 17 April 2019

• 8 May 2019

• SuSiE notes and implementation

• 26 June 2019

• 3 July 2019

• 15 July 2019

• 24 July 2019

• Some notes before identifying the problems with my code

• 31 July 2019

• 14 August 2019

• Final checks

Prior re-weighting (brief revisit to fine-mapping)

• 28 Aug 2019

• 11 Sept 2019

• 16 Sept 2019

• 2 Oct 2019

Functional genomics (2nd year PhD)

• Basics

• eQTLs, ASE and colocalisation

• GWAS to function

• Chromatin conformation

Peaky+

• 10 Oct 2019

• 17 Oct 2019

Return to functional genomics

• How do Cohesin and CTCF Fold DNA in Mammalian Genomes

• Technologies to study spatial genome organisation

• 31 Oct 2019

• 14 Nov 2019

• Quantile Regression

• 5 Dec 2019

• 12 Dec 2019

• 19 Dec 2019

• Genomic control

• End of 2019 summary

cfdr method for functional annotations

• 9th Jan 2020

• 17th Jan 2020

• 24th Jan 2020

• 30th Jan 2020

• 6th Feb 2020

• 12th Feb 2020

• 5th March 2020

• 12th March 2020

• 19th March 2020

• 26th March 2020

• 2nd April 2020

• 9nd April 2020

• 17th April 2020

• 24th April 2020

• 30th April 2020

• 7th May 2020

• 14th May 2020

• 21st May 2020

• 28th May 2020

• 2nd June 2020

• 11th June 2020

• 18th June 2020

• 25th June 2020

• 2nd July 2020

• 9th July 2020

• 16th July 2020

• 23rd July 2020

• 30th July 2020

• 6th August 2020

• 13th August 2020

• 20th August 2020

• 3rd September 2020

• 10th September 2020

• 8th October 2020

• 12th November 2020

• 18th November 2020

• 26th November 2020

• 3rd December 2020

• 14th Jan 2021

• 21st Jan 2021

• 28th Jan 2021

• 11th Feb 2021

• 18th Feb 2021

• 25th Feb 2021

• 4th March 2021

• 8th April 2021

• 6th May 2021

• 17th June 2021

• 1st July 2021

Existing methods:

• Summary

• LD Score Regression

• fgwas

• GREGOR

• GoShifter

• CHEERS

• GARFIELD

• PAINTOR

Extra reading:

• Knockoffs