rTASSEL — Peer-reviewed • Rank 5.6 • Science 95%

rTASSEL: An R interface to TASSEL for analyzing genomic diversity - Published in JOSS (2022)

Correlation Trait Loci (CTL) mapping — Peer-reviewed • Rank 2.7 • Science 93%

Correlation Trait Loci (CTL) mapping: phenotype network inference subject to genotype - Published in JOSS (2016)

locuszoom • Rank 14.6 • Science 75%

A Javascript/d3 embeddable plugin for interactively visualizing statistical genetic data from customizable sources.

haptools • Rank 10.1 • Science 65%

Ancestry and haplotype aware simulation of genotypes and phenotypes for complex trait analysis

snpsea • Rank 3.7 • Science 67%

:bar_chart: Identify cell types and pathways affected by genetic risk loci.

hail • Rank 24.2 • Science 46%

Cloud-native genomic dataframes and batch computing

qqman • Rank 18.0 • Science 46%

An R package for creating Q-Q and manhattan plots from GWAS results

gwas • Rank 5.8 • Science 57%

UNDER CONSTRUCTION: A pipeline for Genome Wide Association Studies

poolgen • Rank 4.2 • Science 57%

Quantitative and population genetics analyses of populations, pools, half-sib/full-sib families, and polyploids

pcsstools • Rank 8.3 • Science 49%

Tools for regression using pre-computed summary statistics

mungesumstats • Rank 7.0 • Science 49%

Rapid standardisation and quality control of GWAS or QTL summary statistics

hierfstat • Rank 15.6 • Science 36%

the hierfstat package

BGData • Rank 11.1 • Science 39%

A Suite of Packages for Analysis of Big Genomic Data

quincunx • Rank 9.0 • Science 39%

quincunx: an R package to query, download and wrangle PGS Catalog data

https://github.com/aehrc/variantspark • Rank 11.2 • Science 36%

machine learning for genomic variants

statgenGWAS • Rank 13.7 • Science 26%

See https://biometris.github.io/statgenGWAS for a full description

qtlizer • Rank 2.5 • Science 33%

getmstatistic • Rank 12.5 • Science 23%

Quantifying Systematic Heterogeneity in Meta-Analysis

GWASinlps • Rank 5.6 • Science 23%

R package for Non-local Prior Based Iterative Variable Selection for Genome-Wide Association Studies, or Other High-Dimensional Data

prewas • Rank 5.0 • Science 23%

R package to perform data pre-processing for more informative bacterial GWAS

saigegds • Rank 4.0 • Science 23%

Scalable Implementation of generalized mixed models using GDS files in Phenome-Wide Association Studies

adjclust • Rank 11.4 • Science 10%

Adjacency-constrained hierarchical clustering of a similarity matrix

miamiplot • Science 44%

An R package for creating ggplot2 based miami plots.

https://github.com/danymukesha/pleior • Science 26%

Identify, analyze and interpret pleiotropic genetic variants (SNPs associated with multiple traits and diseases) using GWAS data, with a focus on understanding shared biological mechanisms.

DAK • Science 10%

Explaining the genetic causality for complex diseases by deep association kernel learning

viprs • Science 44%

Variational Inference of Polygenic Risk Scores

hbf-gwas-scripts • Science 44%

Genome-wide association study of fetal hemoglobin (HbF) in sickle cell anemia patients from Cameroon and other African ancestry populations

nf-gwas • Science 65%

A nextflow pipeline to perform state-of-the-art genome-wide association studies.

sme • Science 49%

A fast and scalable method to detect epistasis in complex traits from biobank-scale studies

cleansumstats • Science 54%

Convert GWAS sumstat files into a common format with a common reference for positions, rsids and effect alleles.

ggfastman • Science 67%

Fast manhattenplots using ggplot2

containers • Science 67%

CoMorMent-Containers

l0 • Science 26%

Scalable reinforcement learning pipeline for general-purpose agents. Build and train agents using the Notebook Agent (NB-Agent) in a flexible environment. 🐙🚀

neurodegeneration_meta-analysis • Science 26%

A developing platform for analysis of genotype data and GWAS summary statistics on neurodegenerative diseases

https://github.com/biometris/statgenqtlxt • Science 26%

See https://biometris.github.io/statgenQTLxT for a full description

magenpy • Science 31%

Modeling and Analysis of (Statistical) Genetics data in python