Discover statgen/fivex Open Source project

A Javascript/d3 embeddable plugin for interactively visualizing statistical genetic data from customizable sources.

151

locuszoom

Genetic multiplexing of barcoded single cell RNA-seq

149

demuxlet

bamUtil

SLURM-examples

locuszoom-standalone

Create regional association plots from GWAS or meta-analysis

Minimac4

Useful set of classes for creating statistical genetic programs.

libStatGen

A suite of population scale analysis tools for single-cell genomics data including implementation of Demuxlet / Freemuxlet methods and auxilary tools

popscle

fastQValidator

EPACTS

emeraLD

tools to efficiently retrieve and calculate LD

Genomes on the Cloud, Mapping & Variant Calling Pipelines

gotcloud

verifyBamID

Interface to various variant calling formats.

savvy

Meta-analysis of genomewide association scans

METAL

topmed_variant_calling

Fast API server for calculating linkage disequilibrium

LDServer

Software to help identify overlap between association scan results and GWAS hit catalogs.

swiss

encore

Encore Analysis Server

Genetic correlation calculation pipeline via summary statistics for PheWeb

pheweb-rg-pipeline

Nextflow

topmed_freeze3_calling

TOPMed Freeze 3 variant calling pipeline

bravo

Deprecated. See new version: https://github.com/statgen/bravo_api - BRowse All Variants Online

HTML

raremetal

A flexible tool for meta-analysis

Make interactive LocusZoom plots from a local GWAS file

localzoom

Vue

ruth

Robust Unified Hardy-Weinberg Equilibrium Test

R package for computing Polygenic Risk Scores (PRS)

Rprs

Raremetal2

(beta) An updated version of meta-analysis software Raremetal.

Locating Ancestry from SEquence Reads

LASER

Credible set determination in GWAS results

gwas-credible-sets

qplot

An R package to interact with the Encore analysis server

csg-utils

Perl

encore-client-r

HVCF

Set of tools for dealing with BAM Stats files.

statsTools

hds-util

JS implementation of rare variant aggregation tests

raremetal.js

minimac

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/qplot

statgen

Simple Tools using the statgen library.

statgenTools

Tag(ging) It(erative) of SNVs in multiple populations

TagIt

Example repository for having multiple tools in one repository.

SampleTools

Makefile

gvs-public

The public base of gvs, which does not contain any secret keys or emails

samtools v0.1.7a with updated bgzf logic and "calmd" logic

csg-storage-slots

Perl

SampleProgram

Makefile

samtools-0.1.7a-hybrid

locuszoom-api

Flask server code for LocusZoom APIs

GLP to create SNP tables for submission to dbSNP

table2dbSNP

A pre-made machine image with a set of commonly used tools

topmed-alignment

Perl

statgen-tools-image

Shell

cloud-align

Script for aligning on dynamically provisioned VM's.

TypeScript

terraform-imputation-server-modules

Wrapper modules for Imputation Server infrastructure

HCL

bravo_api

Server side data processing and retrieval endpoints for BRAVO

A set of tools for accessing and manipulating CRAM files

cram-access-tools

Dockerfile

locuszoom-hosted

A web service to upload and share GWAS results with LocusZoom.js

sequencing_comparison

Javascript modules for 2D and 3D Interactive Visualization (23IV) using WebGL.

23IV

Python library for text-based GUI

dialogs

phegraph

HTML

vcfUtil