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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 scanstopmed_variant_calling
LDServer
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.raremetal.js
JS implementation of rare variant aggregation testshds-util
minimac
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.SampleTools
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 toolsterraform-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.jscloud-align
Script for aligning on dynamically provisioned VM's.sequencing_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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