Explore @statgen Open Source projects

Center for Statistical Genetics (@statgen)

statgen

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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-seq

bamUtil

SLURM-examples

locuszoom-standalone

Create regional association plots from GWAS or meta-analysis

Minimac4

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 tools

fastQValidator

Validate FastQ Files

EPACTS

emeraLD

tools to efficiently retrieve and calculate LD

gotcloud

Genomes on the Cloud, Mapping & Variant Calling Pipelines

verifyBamID

savvy

Interface to various variant calling formats.

METAL

Meta-analysis of genomewide association scans

topmed_variant_calling

LDServer

Fast API server for calculating linkage disequilibrium

fivex

Interactive eQTL visualizations

swiss

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

encore

Encore Analysis Server

pheweb-rg-pipeline

Genetic correlation calculation pipeline via summary statistics for PheWeb

topmed_freeze3_calling

TOPMed Freeze 3 variant calling pipeline

bravo

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

raremetal

A flexible tool for meta-analysis

localzoom

Make interactive LocusZoom plots from a local GWAS file

ruth

Robust Unified Hardy-Weinberg Equilibrium Test

Rprs

R package for computing Polygenic Risk Scores (PRS)

Raremetal2

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

LASER

Locating Ancestry from SEquence Reads

gwas-credible-sets

Credible set determination in GWAS results

qplot

csg-utils

encore-client-r

An R package to interact with the Encore analysis server

HVCF

statsTools

Set of tools for dealing with BAM Stats files.

hds-util

raremetal.js

JS implementation of rare variant aggregation tests

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/qplot

statgenTools

Simple Tools using the statgen library.

TagIt

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

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 emails

csg-storage-slots

SampleProgram

samtools-0.1.7a-hybrid

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

locuszoom-api

Flask server code for LocusZoom APIs

table2dbSNP

GLP to create SNP tables for submission to dbSNP

topmed-alignment

statgen-tools-image

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

cloud-align

Script for aligning on dynamically provisioned VM's.

terraform-imputation-server-modules

Wrapper modules for Imputation Server infrastructure

bravo_api

Server side data processing and retrieval endpoints for BRAVO

cram-access-tools

A set of tools for accessing and manipulating CRAM files

locuszoom-hosted

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

sequencing_comparison

23IV

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

dialogs

Python library for text-based GUI

phegraph

vcfUtil