Explore @chanzuckerberg Open Source projects

Chan Zuckerberg Initiative (@chanzuckerberg)

chanzuckerberg

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7.6 %

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sorbet-rails

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

cellxgene

An interactive explorer for single-cell transcriptomics data

czi-prosemirror

Rich Text Editor built with React and ProseMirror

fogg

Manage Infrastructure as Code with less pain.

shasta

[MOVED] Moved to paoloshasta/shasta. De novo assembly from Oxford Nanopore reads

MedMentions

A corpus of Biomedical papers annotated with mentions of UMLS entities.

miniwdl

Workflow Description Language developer tools & local runner

cellxgene-census

CZ CELLxGENE Discover Census

Jupyter Notebook

czid-web

Infectious Disease Sequencing Platform

software-mentions

Jupyter Notebook

single-cell-data-portal

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

cztack

The CZI infrastructure stack.

blessclient

Go client to negotiate SSH certificates

axe-storybook-testing

Command line interface for testing Storybook stories for accessibility.

napari-hub

Discover, install, and share napari plugins

ChemDisGene

Bio relation extraction labeled dataset

s3parcp

Faster than s3cp

single-cell-curation

Code and documentation for the curation of cellxgene datasets

czid-workflows

Portable WDL workflows for CZ ID production pipelines

redis-memo

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

redcord

A Ruby ORM like Active Record, but for Redis.

idseq-workflows

Portable WDL workflows for IDseq production pipelines

taxoniq

Taxon Information Query - fast, offline querying of NCBI Taxonomy and related data

sorbet-coerce

A type coercion lib works with Sorbet's static type checker and type definitions

ExpressionMatrix2

Software for exploration of gene expression data from single-cell RNA sequencing.

edu-design-system

Design system for Education Projects

chalice-app-template

An AWS Lambda serverless app template with Terraform deployment management

czid-dag

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

sci-components

2021 Science Design System Component Library

scRNA-python-workshop

All the action is on the course webpage -->

Jupyter Notebook

alhazen

AI agents + toolkits for scientific knowledge

Jupyter Notebook

czid-cli

CZID (formerly IDseq) infectious disease command-line interface

software-impact-hackathon-2023

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

happy

Happy Path Deployment Tool

cellxgene-documentation

Documentation for the cellxgene product

aws-oidc

AWS OIDC Federation

cryoet-data-portal

CryoET Data Portal

rotator

Rotator is a tool for rotating credentials on a regular schedule.

czid-dedup

deduplicate FASTA and FASTQ files

czgenepi

terraform-provider-bless

Terraform provider to automate the creation of BLESS deployments

scEvalsJam

Jupyter Notebook

czi-oss-training

Training Materials for Good Open Source Citizenship

s3mi

Transfer big files fast between S3 and EC2. Pronounced "semi".

single-cell-explorer

Hosted version of cellxgene

napari-plugin-alfa-cohort

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

pyrepl

JS/Python execution bridge

software-mention-extraction

Software mention extraction and linking from scientific articles

Jupyter Notebook

napari-cryoet-data-portal

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

prometheus-demo

Simulates monitoring HTTP microservice and short-lived job metrics

ruby-prof-speedscope

A ruby-prof printer for the speedscope.app trace viewer.

galago

Interpretation aids for genomic epidemiology

go-misc

miscellaneous go code

scoreboard

minimalist web app for comparing algorithm performance on benchmark data

idseq-cli

IDseq infectious disease command-line interface

open-science

curated links and customized materials to support biomedical researchers in implementing open science approaches

swipe

SFN-WDL infrastructure for pipeline execution - a template repository and Terraform module for SFN-WDL based projects

idseq-bench

IDseq infectious disease benchmarking tools

napari-hub-collections

DEPRECATED: collections of plugins for the napari hub

bff

Breaking, Feature, Fix - a tool for managing semantic versioning

gs

A small, user-friendly Google Cloud Storage CLI client

ontology-ui

Ontology visualizer

frontend-libs

Monorepo of TypeScript projects for the Chan Zuckerberg Initiative.

miniwdl-plugins

MiniWDL plugins

concept_discovery

spatial-warehouse

Investigation into spatial data and data schema

Jupyter Notebook

docs-editor

rich text editor for education purpose.

reaper

DRSM-corpus

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

full-text-mining-ner

Open Source Code for Extraction of Methods and Datasets from Biomedical Papers

github-actions

A collection of re-usable GitHub Actions

single-cell

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

nbconvert-service

A very light API wrapper around nbconvert

napari-hub-cli

This is a CLI for the napari hub

czid-platformics

wdl-cell-ranger

Run Cell Ranger pipelines using WDL and Cromwell

cellxgene-compbio-methods

Jupyter Notebook

shasta-docs

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

napari-segmentation-workshop

workshop materials for performing cell segmentation in napari

cellxgene-ontology-guide

napari.dev

homebrew-tap

chained-aws-lambda

ncbi-tool-cliclient

CLI client for NCBI data tool

ncbi-tool-sync

Sync component for NCBI data tool

czecs

CLI deployment tool for AWS Elastic Container Service

czLandscapingTk

Landscaping analysis tools for publicly available scientific knowledge sources.

scatter-demo

demo scatter plot using webgl and regl

go-kmsauth

Port kmsauth to go

safe_type

Type Coercion & Type Enhancement

awesome-data-insights-projects

platformics

Codegen Python GraphQL Entity Framework

miniwdl-viz

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

shasta-docker

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

mini-ete3-js

npm package for basic phylogenetics functionality in the browser

cellxgene-manuscript-2023

Code and data to reproduce analyses in the 2023 cellxgene manuscript

Jupyter Notebook

CZ-PR-bot

A Github bot for streamlined PR reviews

ncbi-tool-search

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

crc-squared

light speed crc32c checksums

go-travis-wait

A better wrapper for travis_wait