Chan Zuckerberg Initiative (@chanzuckerberg)

Top repositories

1

sorbet-rails

A set of tools to make the Sorbet typechecker work with Ruby on Rails seamlessly.
Ruby
636
star
2

cellxgene

An interactive explorer for single-cell transcriptomics data
JavaScript
622
star
3

czi-prosemirror

Rich Text Editor built with React and ProseMirror
JavaScript
331
star
4

fogg

Manage Infrastructure as Code with less pain.
Go
269
star
5

shasta

[MOVED] Moved to paoloshasta/shasta. De novo assembly from Oxford Nanopore reads
C++
269
star
6

MedMentions

A corpus of Biomedical papers annotated with mentions of UMLS entities.
262
star
7

miniwdl

Workflow Description Language developer tools & local runner
Python
175
star
8

cellxgene-census

CZ CELLxGENE Discover Census
Jupyter Notebook
82
star
9

czid-web

Infectious Disease Sequencing Platform
Ruby
72
star
10

software-mentions

Jupyter Notebook
66
star
11

single-cell-data-portal

The data portal supporting the submission, exploration, and management of projects and datasets to cellxgene.
TypeScript
63
star
12

cztack

The CZI infrastructure stack.
HCL
61
star
13

blessclient

Go client to negotiate SSH certificates
Go
60
star
14

axe-storybook-testing

Command line interface for testing Storybook stories for accessibility.
TypeScript
52
star
15

napari-hub

Discover, install, and share napari plugins
TypeScript
51
star
16

ChemDisGene

Bio relation extraction labeled dataset
Python
40
star
17

s3parcp

Faster than s3cp
Go
37
star
18

single-cell-curation

Code and documentation for the curation of cellxgene datasets
Python
37
star
19

czid-workflows

Portable WDL workflows for CZ ID production pipelines
Python
36
star
20

redis-memo

A Redis-based version addressable caching system. Memoize pure functions, aggregated database queries, and 3rd party API calls.
Ruby
33
star
21

redcord

A Ruby ORM like Active Record, but for Redis.
Ruby
32
star
22

idseq-workflows

Portable WDL workflows for IDseq production pipelines
Python
31
star
23

taxoniq

Taxon Information Query - fast, offline querying of NCBI Taxonomy and related data
Python
30
star
24

sorbet-coerce

A type coercion lib works with Sorbet's static type checker and type definitions
Ruby
29
star
25

ExpressionMatrix2

Software for exploration of gene expression data from single-cell RNA sequencing.
C++
29
star
26

edu-design-system

Design system for Education Projects
TypeScript
28
star
27

chalice-app-template

An AWS Lambda serverless app template with Terraform deployment management
Python
28
star
28

czid-dag

Please see https://github.com/chanzuckerberg/czid-workflows for the latest version of CZ ID workflows.
Python
27
star
29

sci-components

2021 Science Design System Component Library
TypeScript
25
star
30

scRNA-python-workshop

All the action is on the course webpage -->
Jupyter Notebook
24
star
31

alhazen

AI agents + toolkits for scientific knowledge
Jupyter Notebook
20
star
32

czid-cli

CZID (formerly IDseq) infectious disease command-line interface
Go
19
star
33

software-impact-hackathon-2023

A collection of projects by participants in CZI's hackathon "Mapping the Impact of Research Software in Science" (October 2023)
18
star
34

happy

Happy Path Deployment Tool
Go
18
star
35

cellxgene-documentation

Documentation for the cellxgene product
17
star
36

aws-oidc

AWS OIDC Federation
Go
15
star
37

cryoet-data-portal

CryoET Data Portal
TypeScript
15
star
38

rotator

Rotator is a tool for rotating credentials on a regular schedule.
Go
15
star
39

czid-dedup

deduplicate FASTA and FASTQ files
Rust
15
star
40

czgenepi

Python
13
star
41

terraform-provider-bless

Terraform provider to automate the creation of BLESS deployments
Go
12
star
42

scEvalsJam

Jupyter Notebook
12
star
43

czi-oss-training

Training Materials for Good Open Source Citizenship
11
star
44

s3mi

Transfer big files fast between S3 and EC2. Pronounced "semi".
Python
11
star
45

single-cell-explorer

Hosted version of cellxgene
TypeScript
11
star
46

napari-plugin-alfa-cohort

Repo for the CZI Imaging Team's napari plugin Alfa Cohort collaboration
11
star
47

pyrepl

JS/Python execution bridge
JavaScript
9
star
48

software-mention-extraction

Software mention extraction and linking from scientific articles
Jupyter Notebook
9
star
49

napari-cryoet-data-portal

A napari plugin to list, preview, and open data from the CZ Imaging Institute's CryoET Data Portal
Python
8
star
50

prometheus-demo

Simulates monitoring HTTP microservice and short-lived job metrics
Python
8
star
51

ruby-prof-speedscope

A ruby-prof printer for the speedscope.app trace viewer.
Ruby
8
star
52

galago

Interpretation aids for genomic epidemiology
TypeScript
8
star
53

go-misc

miscellaneous go code
Go
8
star
54

scoreboard

minimalist web app for comparing algorithm performance on benchmark data
JavaScript
8
star
55

idseq-cli

IDseq infectious disease command-line interface
Python
8
star
56

open-science

curated links and customized materials to support biomedical researchers in implementing open science approaches
JavaScript
8
star
57

swipe

SFN-WDL infrastructure for pipeline execution - a template repository and Terraform module for SFN-WDL based projects
Python
7
star
58

idseq-bench

IDseq infectious disease benchmarking tools
Python
7
star
59

napari-hub-collections

DEPRECATED: collections of plugins for the napari hub
Python
7
star
60

bff

Breaking, Feature, Fix - a tool for managing semantic versioning
Go
6
star
61

gs

A small, user-friendly Google Cloud Storage CLI client
Python
6
star
62

ontology-ui

Ontology visualizer
TypeScript
6
star
63

frontend-libs

Monorepo of TypeScript projects for the Chan Zuckerberg Initiative.
TypeScript
6
star
64

miniwdl-plugins

MiniWDL plugins
Python
6
star
65

concept_discovery

Python
6
star
66

spatial-warehouse

Investigation into spatial data and data schema
Jupyter Notebook
6
star
67

docs-editor

rich text editor for education purpose.
HTML
5
star
68

reaper

Go
5
star
69

DRSM-corpus

An annotated literature corpus for NLP studies of 'Disease Research State' based on different categories of research.
5
star
70

full-text-mining-ner

Open Source Code for Extraction of Methods and Datasets from Biomedical Papers
Python
5
star
71

github-actions

A collection of re-usable GitHub Actions
HCL
5
star
72

single-cell

A collection of documents that reflect various design decisions that have been made for the cellxgene project.
4
star
73

nbconvert-service

A very light API wrapper around nbconvert
Python
4
star
74

napari-hub-cli

This is a CLI for the napari hub
Python
4
star
75

czid-platformics

Python
4
star
76

wdl-cell-ranger

Run Cell Ranger pipelines using WDL and Cromwell
Python
4
star
77

cellxgene-compbio-methods

Jupyter Notebook
3
star
78

shasta-docs

[DEPRECATED] Shasta github.io repo for user guides, etc.
3
star
79

napari-segmentation-workshop

workshop materials for performing cell segmentation in napari
TeX
3
star
80

cellxgene-ontology-guide

Python
2
star
81

napari.dev

HTML
2
star
82

homebrew-tap

Ruby
2
star
83

chained-aws-lambda

Python
2
star
84

ncbi-tool-cliclient

CLI client for NCBI data tool
Go
2
star
85

ncbi-tool-sync

Sync component for NCBI data tool
Go
2
star
86

czecs

CLI deployment tool for AWS Elastic Container Service
Go
2
star
87

czLandscapingTk

Landscaping analysis tools for publicly available scientific knowledge sources.
Python
2
star
88

scatter-demo

demo scatter plot using webgl and regl
JavaScript
2
star
89

go-kmsauth

Port kmsauth to go
Go
2
star
90

safe_type

Type Coercion & Type Enhancement
Ruby
2
star
91

awesome-data-insights-projects

2
star
92

platformics

Codegen Python GraphQL Entity Framework
Python
2
star
93

miniwdl-viz

A library to decompose WDL files into a JSON/YAML, and create a mermaid flowchart
WDL
2
star
94

shasta-docker

[DEPRECATED] This repository contains the code and configuration required to create Docker images for Shasta on different platforms.
Python
2
star
95

mini-ete3-js

npm package for basic phylogenetics functionality in the browser
TypeScript
1
star
96

cellxgene-manuscript-2023

Code and data to reproduce analyses in the 2023 cellxgene manuscript
Jupyter Notebook
1
star
97

CZ-PR-bot

A Github bot for streamlined PR reviews
JavaScript
1
star
98

ncbi-tool-search

Collection of script-style utility functions for the NT/NR search mapping research.
Go
1
star
99

crc-squared

light speed crc32c checksums
Go
1
star
100

go-travis-wait

A better wrapper for travis_wait
Shell
1
star