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Search results for python gwas

33 search results found

Cloud-native genomic dataframes and batch computing

Statistical genetics toolkit

Python command line tool for Multi-Trait Analysis of GWAS (MTAG)

SEER, reimplemented in python 🐍🔮

Tiledb Vcf ⭐ 79

Efficient variant-call data storage and retrieval library using the TileDB storage library.

Pan-genome wide association studies

PolyFun (POLYgenic FUNctionally-informed fine-mapping)

Vcf2gwas ⭐ 62

Python API for comprehensive GWAS analysis using GEMMA

GORpipe is a tool based on a genomic ordered relational architecture and allows analysis of large sets of genomic and phenotypic tabular data using declarative query language, in a parallel execution engine.

A Python package for creating high-quality manhattan and Q-Q plots from GWAS results.

Sumstatsrehab ⭐ 20

GWAS summary statistics files QC tool

Twas_sim ⭐ 19

Using real genotype data, simulate a complex trait as a function of latent expression, fit eQTL weights in independent data, and perform GWAS/TWAS on complex trait.

Kgwasflow ⭐ 19

kGWASflow is a Snakemake workflow for performing k-mers-based GWAS.

Permgwas ⭐ 17

Efficient Permutation-based GWAS for Normal and Skewed Phenotypic Distributions

Framework for efficient high-dimensional association analyses.

Heritability, genetic correlation and functional enrichment estimation for case-control studies

Gentropy ⭐ 13

Open Targets python framework for post-GWAS analysis

Haptools ⭐ 13

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

A package for detecting epistasis by machine learning

Software to perform multi-ancestry SNP fine-mapping on molecular data

Nonlinear Causal ⭐ 10

nl-causal: nonlinear causal inference based on IV regression in Python

GWAS QC, PCA, haplotype phasing, genotype imputation

Multi Kernel Linear Mixed Models for Complex Phenotype Prediction

Glow Solution Accelerator ⭐ 10

Genome-wide association studies identify genetic variations associated with a target disease or trait. Researchers and clinicians can use this information to better detect, treat and prevent chronic health conditions. This Solution Accelerator notebook builds on top of Glow

Bin-map Constructer For RILs

Tad_pathways_pipeline ⭐ 7

Pipeline to implement a "TAD_Pathways" analysis. Discover candidate genes based on association signals in TADs

Bayesian Gene Heritability Analysis from GWAS summary statistics

Quality Control Summary Pipeline for Array-based Genome Studio Projects (idats, raw genotype quality)

A k-mer counter that streams gene-cluster specific k-mers, while keeping k-mer positional information. Useful for microbial GWAS analyses with higher interpretability.

Pygwasvcf ⭐ 5

Python library for reading GWAS summary statistics in GWAS-VCF files

Coupled Mixed Model

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