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pheweb
A tool to build a website to browse hundreds or thousands of GWAS.locuszoom
A Javascript/d3 embeddable plugin for interactively visualizing statistical genetic data from customizable sources.demuxlet
Genetic multiplexing of barcoded single cell RNA-seqbamUtil
SLURM-examples
locuszoom-standalone
Create regional association plots from GWAS or meta-analysisMinimac4
libStatGen
Useful set of classes for creating statistical genetic programs.popscle
A suite of population scale analysis tools for single-cell genomics data including implementation of Demuxlet / Freemuxlet methods and auxilary toolsfastQValidator
Validate FastQ FilesEPACTS
emeraLD
tools to efficiently retrieve and calculate LDgotcloud
Genomes on the Cloud, Mapping & Variant Calling PipelinesverifyBamID
savvy
Interface to various variant calling formats.METAL
Meta-analysis of genomewide association scansLDServer
Fast API server for calculating linkage disequilibriumfivex
Interactive eQTL visualizationsswiss
Software to help identify overlap between association scan results and GWAS hit catalogs.encore
Encore Analysis Serverpheweb-rg-pipeline
Genetic correlation calculation pipeline via summary statistics for PheWebtopmed_freeze3_calling
TOPMed Freeze 3 variant calling pipelinebravo
Deprecated. See new version: https://github.com/statgen/bravo_api - BRowse All Variants Onlineraremetal
A flexible tool for meta-analysislocalzoom
Make interactive LocusZoom plots from a local GWAS fileruth
Robust Unified Hardy-Weinberg Equilibrium TestRprs
R package for computing Polygenic Risk Scores (PRS)Raremetal2
(beta) An updated version of meta-analysis software Raremetal.LASER
Locating Ancestry from SEquence Readsgwas-credible-sets
Credible set determination in GWAS resultsqplot
qplotcsg-utils
encore-client-r
An R package to interact with the Encore analysis serverHVCF
statsTools
Set of tools for dealing with BAM Stats files.hds-util
raremetal.js
JS implementation of rare variant aggregation testsminimac
statgen
This repository has been deprecated and replaced with libStatGen, https://github.com/statgen/libStatGen and the tools have been broken out to other repositories including: https://github.com/statgen/bamUtil and https://github.com/statgen/qplotstatgenTools
Simple Tools using the statgen library.TagIt
Tag(ging) It(erative) of SNVs in multiple populationsSampleTools
Example repository for having multiple tools in one repository.gvs-public
The public base of gvs, which does not contain any secret keys or emailscsg-storage-slots
SampleProgram
samtools-0.1.7a-hybrid
samtools v0.1.7a with updated bgzf logic and "calmd" logiclocuszoom-api
Flask server code for LocusZoom APIstable2dbSNP
GLP to create SNP tables for submission to dbSNPtopmed-alignment
statgen-tools-image
A pre-made machine image with a set of commonly used toolscloud-align
Script for aligning on dynamically provisioned VM's.terraform-imputation-server-modules
Wrapper modules for Imputation Server infrastructurebravo_api
Server side data processing and retrieval endpoints for BRAVOcram-access-tools
A set of tools for accessing and manipulating CRAM fileslocuszoom-hosted
A web service to upload and share GWAS results with LocusZoom.jssequencing_comparison
23IV
Javascript modules for 2D and 3D Interactive Visualization (23IV) using WebGL.dialogs
Python library for text-based GUIphegraph
vcfUtil
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