Center for Statistical Genetics (@statgen)

Top repositories

1

pheweb

A tool to build a website to browse hundreds or thousands of GWAS.
Python
151
star
2

locuszoom

A Javascript/d3 embeddable plugin for interactively visualizing statistical genetic data from customizable sources.
JavaScript
149
star
3

demuxlet

Genetic multiplexing of barcoded single cell RNA-seq
C++
115
star
4

bamUtil

C++
83
star
5

SLURM-examples

Python
80
star
6

locuszoom-standalone

Create regional association plots from GWAS or meta-analysis
Python
56
star
7

Minimac4

C++
53
star
8

libStatGen

Useful set of classes for creating statistical genetic programs.
C++
49
star
9

popscle

A suite of population scale analysis tools for single-cell genomics data including implementation of Demuxlet / Freemuxlet methods and auxilary tools
C++
43
star
10

fastQValidator

Validate FastQ Files
C++
35
star
11

EPACTS

C++
33
star
12

emeraLD

tools to efficiently retrieve and calculate LD
C++
32
star
13

gotcloud

Genomes on the Cloud, Mapping & Variant Calling Pipelines
C++
31
star
14

verifyBamID

C++
27
star
15

savvy

Interface to various variant calling formats.
C++
25
star
16

METAL

Meta-analysis of genomewide association scans
C++
19
star
17

topmed_variant_calling

C++
17
star
18

LDServer

Fast API server for calculating linkage disequilibrium
C++
13
star
19

fivex

Interactive eQTL visualizations
Vue
13
star
20

swiss

Software to help identify overlap between association scan results and GWAS hit catalogs.
Python
13
star
21

encore

Encore Analysis Server
Python
13
star
22

pheweb-rg-pipeline

Genetic correlation calculation pipeline via summary statistics for PheWeb
Nextflow
12
star
23

topmed_freeze3_calling

TOPMed Freeze 3 variant calling pipeline
C
10
star
24

bravo

Deprecated. See new version: https://github.com/statgen/bravo_api - BRowse All Variants Online
HTML
8
star
25

raremetal

A flexible tool for meta-analysis
C++
7
star
26

localzoom

Make interactive LocusZoom plots from a local GWAS file
Vue
7
star
27

ruth

Robust Unified Hardy-Weinberg Equilibrium Test
C++
6
star
28

Rprs

R package for computing Polygenic Risk Scores (PRS)
R
6
star
29

Raremetal2

(beta) An updated version of meta-analysis software Raremetal.
C++
5
star
30

LASER

Locating Ancestry from SEquence Reads
C++
5
star
31

gwas-credible-sets

Credible set determination in GWAS results
JavaScript
4
star
32

qplot

qplot
C++
3
star
33

csg-utils

Perl
2
star
34

encore-client-r

An R package to interact with the Encore analysis server
R
2
star
35

HVCF

C++
2
star
36

statsTools

Set of tools for dealing with BAM Stats files.
C++
2
star
37

hds-util

C++
2
star
38

raremetal.js

JS implementation of rare variant aggregation tests
JavaScript
2
star
39

minimac

C++
2
star
40

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
C++
2
star
41

statgenTools

Simple Tools using the statgen library.
C++
1
star
42

TagIt

Tag(ging) It(erative) of SNVs in multiple populations
C++
1
star
43

SampleTools

Example repository for having multiple tools in one repository.
Makefile
1
star
44

gvs-public

The public base of gvs, which does not contain any secret keys or emails
Python
1
star
45

csg-storage-slots

Perl
1
star
46

SampleProgram

Makefile
1
star
47

samtools-0.1.7a-hybrid

samtools v0.1.7a with updated bgzf logic and "calmd" logic
C
1
star
48

locuszoom-api

Flask server code for LocusZoom APIs
Python
1
star
49

table2dbSNP

GLP to create SNP tables for submission to dbSNP
C++
1
star
50

topmed-alignment

Perl
1
star
51

statgen-tools-image

A pre-made machine image with a set of commonly used tools
Shell
1
star
52

cloud-align

Script for aligning on dynamically provisioned VM's.
TypeScript
1
star
53

terraform-imputation-server-modules

Wrapper modules for Imputation Server infrastructure
HCL
1
star
54

bravo_api

Server side data processing and retrieval endpoints for BRAVO
Python
1
star
55

cram-access-tools

A set of tools for accessing and manipulating CRAM files
Dockerfile
1
star
56

locuszoom-hosted

A web service to upload and share GWAS results with LocusZoom.js
Python
1
star
57

sequencing_comparison

Python
1
star
58

23IV

Javascript modules for 2D and 3D Interactive Visualization (23IV) using WebGL.
JavaScript
1
star
59

dialogs

Python library for text-based GUI
Python
1
star
60

phegraph

HTML
1
star
61

vcfUtil

C++
1
star