Genetics's repositories
FM-pipeline
FineMapping analysis using GWAS summary statistics
gwasurvivr
GWAS Survival Package in R
MetaGWASToolKit
A ToolKit to perform a Meta-analysis of Genome-Wide Association Studies
polygenic-risk-scores
Script to calculate polygenic risk scores in a genotyped sample using GWAS summary statistics from a disease/trait.
algorithms_and_data_structures
180+ Algorithm & Data Structure Problems using C++
ASMC
Ascertained Sequentially Markovian Coalescent
bcbioRNASeq
Quality control and differential expression for bcbio RNA-seq experiments.
CONFIT
association testing in multiple traits
coreutils
upstream mirror
dlib
A toolkit for making real world machine learning and data analysis applications in C++
DosageConvertor
DosageConvertor is a C++ tool to convert dosage files (in VCF format) from Minimac3/4 to other formats such as MaCH or PLINK.
Eagle
Haplotype phasing software
emeraLD
tools to efficiently retrieve and calculate LD
fatdistnGWAS
Code and data for 'Meta-analysis of genome-wide association studies for body fat distribution in 694,649 individuals of European ancestry'
Gimpute
An efficient genetic data imputation pipeline
LeetCode
:pencil: Python / C++ 11 Solutions of All LeetCode Questions
LocusExplorer
An interactive graphical illustration of genetic associations and their biological context
modern-cpp-tutorial
📚 C++11/14/17 On the Fly
OneLiners
OneLiners
plink-ng
A comprehensive update to the PLINK association analysis toolset. Beta testing of the first new version (1.90), focused on speed and memory efficiency improvements, is finishing up. Future development will revolve around critical extensions to the core file format (multiallelic variants, dosage, phase).
Popcorn
Software for estimating correlation of trait effect sizes across populations
Probabilistic-Programming-and-Bayesian-Methods-for-Hackers
aka "Bayesian Methods for Hackers": An introduction to Bayesian methods + probabilistic programming with a computation/understanding-first, mathematics-second point of view. All in pure Python ;)
PRSice-1
A software package for calculating, applying, evaluating and plotting the results of polygenic risk scores
Sarek
Detect germline or somatic variants from normal or tumour/normal whole-genome sequencing data
snpsea
:bar_chart: Identify cell types and pathways affected by genetic risk loci.
UKBB_ldsc
Sample code for ldsc analyses in UKBB
vcflib
a simple C++ library for parsing and manipulating VCF files, + many command-line utilities