Discover chanzuckerberg/czid-platformics Open Source project

An interactive explorer for single-cell transcriptomics data

636

cellxgene

Rich Text Editor built with React and ProseMirror

622

czi-prosemirror

Manage Infrastructure as Code with less pain.

331

fogg

269

shasta

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

C++

269

MedMentions

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

262

miniwdl

Workflow Description Language developer tools & local runner

CZ CELLxGENE Discover Census

175

cellxgene-census

Infectious Disease Sequencing Platform

czid-web

software-mentions

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

single-cell-data-portal

The CZI infrastructure stack.

cztack

HCL

blessclient

Go client to negotiate SSH certificates

axe-storybook-testing

Command line interface for testing Storybook stories for accessibility.

Discover, install, and share napari plugins

napari-hub

Bio relation extraction labeled dataset

ChemDisGene

Code and documentation for the curation of cellxgene datasets

s3parcp

Faster than s3cp

single-cell-curation

Portable WDL workflows for CZ ID production pipelines

czid-workflows

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

redis-memo

A Ruby ORM like Active Record, but for Redis.

redcord

Portable WDL workflows for IDseq production pipelines

idseq-workflows

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

taxoniq

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

sorbet-coerce

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

ExpressionMatrix2

C++

edu-design-system

Design system for Education Projects

An AWS Lambda serverless app template with Terraform deployment management

chalice-app-template

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

czid-dag

2021 Science Design System Component Library

sci-components

All the action is on the course webpage -->

scRNA-python-workshop

AI agents + toolkits for scientific knowledge

alhazen

CZID (formerly IDseq) infectious disease command-line interface

czid-cli

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 is a tool for rotating credentials on a regular schedule.

rotator

czid-dedup

deduplicate FASTA and FASTQ files

Rust

czgenepi

Terraform provider to automate the creation of BLESS deployments

terraform-provider-bless

scEvalsJam

Training Materials for Good Open Source Citizenship

czi-oss-training

s3mi

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

Hosted version of cellxgene

single-cell-explorer

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

napari-plugin-alfa-cohort

pyrepl

JS/Python execution bridge

Software mention extraction and linking from scientific articles

software-mention-extraction

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

napari-cryoet-data-portal

Simulates monitoring HTTP microservice and short-lived job metrics

prometheus-demo

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

ruby-prof-speedscope

Interpretation aids for genomic epidemiology

galago

minimalist web app for comparing algorithm performance on benchmark data

go-misc

miscellaneous go code

scoreboard

IDseq infectious disease command-line interface

idseq-cli

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

open-science

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

swipe

IDseq infectious disease benchmarking tools

idseq-bench

DEPRECATED: collections of plugins for the napari hub

napari-hub-collections

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

bff

A small, user-friendly Google Cloud Storage CLI client

ontology-ui

Ontology visualizer

Monorepo of TypeScript projects for the Chan Zuckerberg Initiative.

frontend-libs

miniwdl-plugins

concept_discovery

spatial-warehouse

Investigation into spatial data and data schema

rich text editor for education purpose.

docs-editor

HTML

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

A collection of re-usable GitHub Actions

github-actions

HCL

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

This is a CLI for the napari hub

napari-hub-cli

Run Cell Ranger pipelines using WDL and Cromwell

wdl-cell-ranger

cellxgene-compbio-methods

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

shasta-docs

napari-segmentation-workshop

workshop materials for performing cell segmentation in napari

TeX

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.

demo scatter plot using webgl and regl

scatter-demo

Type Coercion & Type Enhancement

go-kmsauth

Port kmsauth to go

safe_type

Codegen Python GraphQL Entity Framework

awesome-data-insights-projects

platformics

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

miniwdl-viz

WDL

shasta-docker

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

npm package for basic phylogenetics functionality in the browser

mini-ete3-js

Code and data to reproduce analyses in the 2023 cellxgene manuscript

cellxgene-manuscript-2023

A Github bot for streamlined PR reviews

CZ-PR-bot