Alternatives and similar repositories for SAIGE

Users that are interested in SAIGE are comparing it to the libraries listed below

• gusevlab / fusion_twas
  methods for functional summary-based imputation
  ☆90Updated 3 years ago
• JonJala / mtag
  Python command line tool for Multi-Trait Analysis of GWAS (MTAG)
  ☆199Updated 2 years ago
• JoniColeman / gwas_scripts
  Codebook from my GWAS cookbook
  ☆193Updated 3 years ago
• chr1swallace / coloc
  Repo for the R package coloc
  ☆183Updated 3 months ago
• bvilhjal / ldpred
  ☆101Updated 3 years ago
• omerwe / polyfun
  PolyFun (POLYgenic FUNctionally-informed fine-mapping)
  ☆125Updated 11 months ago
• PMBio / peer
  A factor analysis package
  ☆102Updated 13 years ago
• statgen / pheweb
  A tool to build a website to browse hundreds or thousands of GWAS.
  ☆188Updated 2 months ago
• RitchieLab / eQTpLot
  Visualization of Colocalization Between eQTL and GWAS Data
  ☆86Updated 3 years ago
• molgenis / systemsgenetics
  Generic Java genotype reader / writer, QTL mapping software, Strand alignment tool
  ☆176Updated 11 months ago
• zhenin / HDL
  High-definition likelihood inference of genetic correlations (HDL)
  ☆123Updated 4 months ago
• zhanxw / rvtests
  Rare variant test software for next generation sequencing data
  ☆141Updated 3 years ago
• broadinstitute / tensorqtl
  Ultrafast GPU-enabled QTL mapper
  ☆196Updated 4 months ago
• boxiangliu / locuscomparer
  LocusCompareR is a R package with visualization tools for comparing two genetic association datasets.
  ☆117Updated 2 years ago
• rgcgithub / regenie
  regenie is a C++ program for whole genome regression modelling of large genome-wide association studies.
  ☆241Updated this week
• choishingwan / PRSice
  A software package for calculating, applying, evaluating and plotting the results of polygenic risk scores
  ☆200Updated last year
• atgu / ukbb_pan_ancestry
  Analyses conducting GWAS across the UKBB diverse superpopulations
  ☆59Updated 3 weeks ago
• eskederks / eMAGMA-tutorial
  A step by step guide on how to use eMAGMA, an approach to conducting eQTL informed gene-based tests.
  ☆72Updated 4 years ago
• Al-Murphy / MungeSumstats
  Rapid standardisation and quality control of GWAS or QTL summary statistics
  ☆87Updated last week
• freeseek / gtc2vcf
  Tools to convert Illumina IDAT/BPM/EGT/GTC and Affymetrix CEL/CHP files to VCF
  ☆161Updated 2 months ago
• getian107 / PRScs
  Polygenic prediction via continuous shrinkage priors
  ☆192Updated 11 months ago
• leelabsg / SKAT
  Sequence kernel association test (SKAT)
  ☆52Updated 3 months ago
• Cloufield / gwaslab
  A Python package for handling and visualizing GWAS summary statistics. https://cloufield.github.io/gwaslab/
  ☆260Updated this week
• saigegit / SAIGE
  Development for SAIGE and SAIGE-GENE(+)
  ☆83Updated this week
• opentargets / genetics-sumstat-harmoniser
  Harmonise GWAS summary statistics against a reference VCF
  ☆41Updated 4 years ago
• davidaknowles / leafcutter
  Annotation-free quantification of RNA splicing. Yang I. Li, David A. Knowles, Jack Humphrey, Alvaro N. Barbeira, Scott P. Dickinson, Hae …
  ☆226Updated last year
• astheeggeggs / PHESANT
  PHESANT - PHEnome Scan ANalysis Tool (pheWAS, Mendelian randomisation (MR)-pheWAS etc.) in UK Biobank
  ☆20Updated 3 years ago
• getian107 / PRScsx
  Cross-population polygenic prediction
  ☆90Updated this week
• hakyimlab / MetaXcan
  MetaXcan software and manuscript
  ☆177Updated 4 months ago
• MRCIEU / gwasglue
  Linking GWAS data to analytical tools in R
  ☆148Updated 3 years ago