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awesome-deep-learning

A curated list of awesome Deep Learning tutorials, projects and communities.

awesome-random-forest

Random Forest - a curated list of resources regarding random forest

bccolocalisation_ajhg_2020

Scripts used for BCAC/GTEx colocalisation analysis

coloc

Repo for the R package coloc

colocalisation

This repo contains a nextflow pipeline to do colocalisation analysis of QTLs against GWASs

colocalization_for_two_traits

Code used for GWAS summary statistics

computational-statistics-with-python

Resources for STA 633 class

courses

Course homepages for some of the courses given at SciLifeLab

demo_amd

drugdevelopr

The drugdevelopR package enables planning of phase II/III drug development programs with optimal sample size allocation and go/no-go decision rules.

exposome_correlation

exposome_variability

Characterzing the exposome variability

gwa_tutorial

A comprehensive tutorial about GWAS and PRS

gwas_scripts

Codebook from my GWAS cookbook

gwastutorial

GWAS tutorial

hdl

High-definition likelihood (HDL) inference of genetic correlations using GWAS summary statistics

hiv_zambia

X-Wide Association Study in HIV+ in Zambia

imix

Integrative genomics using a multivariate mixture model framework

impute-pipe

:shower: Canonical SGE cluster genotype imputation pipeline

impute-tools

Scripts to facilitate imputation of genotypes and subsequent QC.

imputeprepsanger

This repository contains scripts to prepare plink genotype files for imputation on the Sanger server.

imputingwithsangerservice

Pre and post Sanger Service steps with some **very** basic scripts. Early learning.

ldsc

LD Score Regression (LDSC)

liftoverplink

A wrapper for liftOver for converting plink genotype data between different genome reference builds

machinelearning

Machine Learning in Action（机器学习实战）

manhattanplot3d

These notebooks parse GWAS summary statistics and generate 3D Manhattan plots and their projections

meetup

microbiome_helper

An assortment of scripts to help process and automate various microbiome and metagenomic bioinformatic tools.

more-textwrangler-and-bbedit-color-schemes

This is Andrew Hazelden's Collection of TextWrangler and BBEdit Color Schemes

mr-maternal-smoking

Analysis code for proxy gene-by-environment Mendelian randomization of maternal smoking on offspring health