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1kgp_pipeline

algorithmsanddatastructures

My efforts to implement the canonical algorithms one finds on the undergraduate curriculum

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.

exemplary_pipeline

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

fcfdr_pipeline

gps_cpp

C++ code for calculating the GPS statistic.

gps_paper_pipeline

gwas_tools

Pipeline for GWAS summary statistic dataset processing

hackmergesort

Mergesort implemented in Hack assembly language

junit5-experiments

Experimental migration of `ConditionalIgnoreRule` and `TemporaryFolder` to JUnit 5 extensions

ldak_weights_pipeline

Snakemake-based pipeline for generating LDAK weights for use with fcFDR.

locuszoomr

longqc

LongQC is a tool for the data quality control of the PacBio and ONT long reads.

miind

nest-simulator

The NEST simulator

orbtree

Generalized order-statistic tree implementation in C++

pidpipelinecode

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!

squick

Script to simplify Slurm job submission