chanzuckerberg/shasta

This repository has been archived on 14/Oct/2022
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Created over 6 years ago
Updated about 2 years ago

chanzuckerberg/shasta

chanzuckerberg

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

Shasta long read assembler

This repository is no longer in use

The project has moved to github.com/paoloshasta/shasta.

Shasta development continues in the new repository.

New Shasta releases will appear in the Releases page of the new repository.

Old Shasta releases (up to 0.10.0) continue to be available in the Releases page of this repository.

For questions, issues, and discussion on any version of Shasta, please use the Issues page of the new repository.

Here is the old README file for this repository. It is now obsolete.

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.

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

single-cell-tissue-coverage-visualization-prototype