GeneticResources

burden_testing

A collection of scripts to run genome-wide burden testing using MONSTER.

gtex-pipeline

GTEx & TOPMed data production and analysis pipelines

gwas-download

Easily download publicly available GWAS summary statistics.

HOPS

Allows to compute the HOrizontal Pleiotropy Score (HOPS) from summary statistics.

NIPT_WGS

awesome-multitrait-gwas

List of software packages for multi-trait / multiple-trait / multivariate / high-dimensional GWAS

awesome-single-cell

Community-curated list of software packages and data resources for single-cell, including RNA-seq, ATAC-seq, etc.

focus

FOCUS: Fine-mapping Of CaUsal gene Sets

FUMA-webapp

Source code of FUMA GWAS web application

h2-GRE

Scripts for GRE

ibis

Algorithm for rapid, phase-free detection of long identical by descent segments

impute-me

This is the code behind the www.impute.me site. It contains algorithms for imputing personal genomes, as well as a range of custom-made analysis for genetics-based disease and health.

imputeInversion

Scripts to impute inversion regions of interest

Minimac4

mixer

Causal Mixture Model for GWAS summary statistics

mvcovreg

PAINTOR_V3.0

Fast, integrative fine mapping with functional data

pandas-profiling

Create HTML profiling reports from pandas DataFrame objects

PBK-QC-pipeline

Partners Biobank genomics data QC

python_convert

A collection of various utilities for GWAS summary statistics

rss

Regression with Summary Statistics.

s-ldxr

Stratified squared trans-ethnic genetic correlation

scanpy

Single-Cell Analysis in Python. Scales to >1M cells.

scRNA.seq.course

Analysis of single cell RNA-seq data course

seurat

R toolkit for single cell genomics

SINCERA

An R implementation of the SINCERA pipeline for single cell RNA-seq profiling analysis

STAAR

An R package for performing STAAR procedure in whole genome sequencing studies

susieR

R package for "sum of single effects" regression.

SZvariant-synergy

UTMOST

UTMOST (unified test for molecular signatures) is a method for cross-tissue gene expression imputation for transcriptome-wide association analyses.