• LDSC
• LDSR - memory summary statistics.
• LDSR - memory summary statistics.
• GCTB - wide SNPs. It was developed to simultaneously estimate the joint effects of all SNPs and the genetic architecture parameters for a complex trait. There are now extensions to estimate the same bayesian linear model parameters based on summary data.
• GCTA - wide Complex Trait Analysis) is a software package initially developed to estimate the proportion of phenotypic variance explained by all genome-wide SNPs for a complex trait.
• RHE-mc/GENIE - mc is a method to estimate the proportion of phenotypic variance explained by SNPs, and GENIE extends this to model GxE effects
• RHE-mc/GENIE - mc is a method to estimate the proportion of phenotypic variance explained by SNPs, and GENIE extends this to model GxE effects
• BOLT-LMM/BOLT-REML - LMM software package currently consists of two main algorithms, the BOLT-LMM algorithm for mixed model association testing, and the BOLT-REML algorithm for variance components analysis (i.e., partitioning of SNP-heritability and estimation of genetic correlations).
• LDAK/SumHer/PCGC - correlation genotype-correlation) Regression is an alternative to REML when estimating heritability for binary traits (i.e., diseases).
• BOLT-LMM/BOLT-REML - LMM software package currently consists of two main algorithms, the BOLT-LMM algorithm for mixed model association testing, and the BOLT-REML algorithm for variance components analysis (i.e., partitioning of SNP-heritability and estimation of genetic correlations).
• LDAK/SumHer/PCGC - correlation genotype-correlation) Regression is an alternative to REML when estimating heritability for binary traits (i.e., diseases).

Univariate models (heritability/poligenicity/stratified/geneset enrichment etc)

• i-LDSC - LD score (i-LDSC) regression: Model an additional score that measures the amount of non-additive genetic variation that is tagged by each variant in the data.
• i-LDSC - LD score (i-LDSC) regression: Model an additional score that measures the amount of non-additive genetic variation that is tagged by each variant in the data.
• ACLR
• HAMSTA
• MAGMA - set analysis of GWAS data.
• MAGMA - set analysis of GWAS data.

Univariate models (heritability/poligenicity/stratified/geneset enrichment etc)

• HDL - Definition Likelihood (HDL) is a likelihood-based method for estimating genetic correlation using GWAS summary statistics. Compared to LD Score regression (LDSC), It reduces the variance of a genetic correlation estimate by about 60%.
• HDL - Definition Likelihood (HDL) is a likelihood-based method for estimating genetic correlation using GWAS summary statistics. Compared to LD Score regression (LDSC), It reduces the variance of a genetic correlation estimate by about 60%.

Stratified/local genetic correlatons

• LAVA
• LAVA

Ancestry aware Genetic correlations:

• s-ldxr - LDXR` is a method to stratify squared trans-ethnic genetic correlation by genomic annotations from GWAS summary statistics.
• s-ldxr - LDXR` is a method to stratify squared trans-ethnic genetic correlation by genomic annotations from GWAS summary statistics.
• Popcorn
• Popcorn
• mama - based command line tool that meta-analyzes GWAS summary statistics generated from distinct ancestry groups.

Genetic SEM/Factor models

• GenomicSEM
• GenomicSEM
• GUIDE
• FactorGO
• GNA
• FactorGO
• GNA
• partialLDSC - package to estimate partial genetic correlations from GWAS summary statistics, and compare them to their unadjusted counterparts, to quantify the contribution of a given confounder in explaining genetic similarity between conditions.
• partialLDSC - package to estimate partial genetic correlations from GWAS summary statistics, and compare them to their unadjusted counterparts, to quantify the contribution of a given confounder in explaining genetic similarity between conditions.
• trivariate MiXeR
• Gsens
• trivariate MiXeR
• Gsens
• bivarite MiXeR
• bivarite MiXeR

Two sample Mendelian Randomisation

• TwoSampleMR
• TwoSampleMR
• SMR - level data from GWAS and expression quantitative trait loci (eQTL) studies

MR/Genetic architecture hybrid models

• lhcMR - directional causal estimation between a pair of traits, while accounting for the presence of a potential heritable confounder acting on the pair.
• lhcMR - directional causal estimation between a pair of traits, while accounting for the presence of a potential heritable confounder acting on the pair.
• CAUSE
• CAUSE
• LCV
• LCV
• MR-cML - MA, applicable to GWAS summary data.

Mendelian randomization in _cis_

• MR-link-2
• MR-link-2

Mendelian randomization in _cis_

• coloc
• fastENLOC
• coloc
• fastENLOC
• FINEMAP - wide association studies.
• polyfun - informed fine-mapping, **PolyLoc** for polygenic localization of complex trait heritability.
• OPERA - level data.
• SuSiEx - population finemapping using summary statistics and LD reference panels.
• SharePro - level approach to integrate LD modeling and colocalization assessment to account for multiple causal variants in colocalization analysis.

Mendelian randomization in _cis_

• FUSION - wide and regulome-wide association studies (TWAS and RWAS).
• FOCUS - mapping Of CaUsal gene Sets) is software to fine-map transcriptome-wide association study statistics at genomic risk regions

Mendelian randomization in _cis_

• GWASBrewer

Mendelian randomization in _cis_

• HAIL - source, general-purpose, Python-based data analysis tool with additional data types and methods for working with genomic data.
• bigsnpr
• ukbrapR - K-B-wrapper') is an R package for working in the UK Biobank Research Analysis Platform (RAP). The aim is to make it quicker, easier, and more reproducible.
• MungeSumstats
• tidyGWAS
• gwasRtools
• qgg - scale genetic and phenotypic data while **gact** is designed for establishing and populating a comprehensive database focused on genomic associations with complex traits, provies R implementations of popular follow up analysis (LDscore regresison, MAGMA, VEGAS, PoPS, etc).
• bcftools
• GenomicRanges
• bedtools - army knife of tools for a wide-range of genomics analysis tasks. A very fast and easy way to intersect, merge, count, complement, and shuffle genomic intervals from multiple files in widely-used genomic file formats such as BAM, BED, GFF/GTF, VCF

Mendelian randomization in _cis_

• PRSice
• LDpred2 - 2 is one of the dedicated PRS programs which is an R package that uses a Bayesian approach to polygenic risk scoring.
• GCTB - wide SNPs. It was developed to simultaneously estimate the joint effects of all SNPs and the genetic architecture parameters for a complex trait.

Mendelian randomization in _cis_

• ieugwasr
• GWAScatalog API - 11-20, the GWAS Catalog contains 7083 publications, 692444 top associations and 96947 full summary statistics.
• GWAS atlas - based) results, SNP heritability and genetic correlations with other GWAS in the database.
• S4 programs

Mendelian randomization in _cis_

• gnomAD browser
• Open Targets Platform
• genebass - based association statistics, made available to the public. The dataset encompasses 4,529 phenotypes with gene-based and single-variant testing across 394,841 individuals with exome sequence data from the UK Biobank.
• All by All - based and single-variant associations across nearly 250,000 whole genome sequences