Tom Willis's repositories
GWAS_tools
Pipeline for GWAS summary statistic dataset processing
bayNorm_papercode
code for producing figures in bayNorm
cfdr
Implements conditional false-discovery rate hypothesis testing, used to perform high-dimensional hypothesis tests. Requires a set of summary statistics in an experiment of interest, and 'levers' on a second set of summary statistics at the same variables for a second experiment. Enables frequentist hypothesis testing with overall strong control of false-discovery rate. Can use several estimators of the cFDR function.
cfdr_pipeline
Pipeline to generate all results in manuscript 'Accurate error control in high dimensional association testing using conditional false discovery rates', by James Liley and Chris Wallace
cpp
Repo for code written when first learning C++ and Qt.
fastman
An R package for fast and efficient visualizing of GWAS results using Q-Q and Manhattan plots directly from PLINK output files.
fcfdr
R package for flexible cFDR (fcfdr)
fcfdr_manuscript
Repo to reproduce results from flexible cFDR manuscript
HackMergesort
Mergesort implemented in Hack assembly language
ldak_weights_pipeline
Snakemake-based pipeline for generating LDAK weights for use with fcFDR.
LongQC
LongQC is a tool for the data quality control of the PacBio and ONT long reads.
nest-simulator
The NEST simulator
orbtree
Generalized order-statistic tree implementation in C++
pidProjCode
Utility code for PID project.
rapidcsv
C++ CSV parser library
scRNAseq
Clone of the Bioconductor repository for the scRNAseq package.
simGWAS
Simulating the expected output from a GWAS with a given causal model.
snakemake
This is the development home of the workflow management system Snakemake. For general information, see
spacemacs
A community-driven Emacs distribution - The best editor is neither Emacs nor Vim, it's Emacs *and* Vim!
topr
topr is a collection of plotting functions for visualizing and exploring genetic association results. Association results from multiple phenotypes can be viewed simultaneously, over the entire genome (Manhattan plot) or in the more detailed regional view.
zinb_analysis
Data analysis and simulations for the ZINB-WaVE paper