Scientific Tools and Resources

Zebrahub is a multimodal, single-cell RNA sequencing atlas of vertebrate development at single-embryo resolution, using zebrafish as a model organism.

OpenCell

OpenCell is a proteome-scale collection of protein localization and interaction measurements in human cells.

PoMeLo

A novel bioinformatic approach for identifying metabolic vulnerabilities of pathogens to Inform host-directed therapeutics.

CZ CELLxGENE

An interactive data explorer for single-cell datasets that leverages modern web development techniques to enable fast visualizations of at least 1 million cells, enabling data exploration.

CZ ID

CZ ID is a hypothesis-free global software platform that helps scientists identify pathogens in metagenomic sequencing data.

napari

napari is a community-built, Python-based, open source tool designed for browsing, annotating, and analyzing large multi-dimensional images. The CZ Biohub and the Chan Zuckerberg Initiative (CZI) collaborate with napari, and CZI built the napari hub to help users find plugins to solve their analysis needs.

Rapid Response resources

mNGS protocols and training materials that were developed in collaboration with the Genomics and Sequencing Platform at CZ Biohub and the CZ ID team at the Chan Zuckerberg Initiative.

DaXi

A new single-objective design that is capable of imaging large samples, with a large imaging volume, uncompromised image resolution and speed, and multi-view imaging.

Tabula Muris Senis

A comprehensive compendium of single-cell transcriptomic data from the model organism Mus musculus.

Tabula Sapiens

Tabula Sapiens is a benchmark, first-draft human cell atlas of nearly 500,000 cells.

Tabula Muris

A compendium of single-cell transcriptome data from the mouse.

COVID Tissue Atlas

The COVID Tissue Atlas enables the investigation of both cell type-specific and cross-organ transcriptional responses to COVID-19, providing insights into the molecular networks affected by the disease and highlighting novel potential targets for therapies and drug development.

cytoself

Self-supervised models for encoding protein localization patterns from microscopy images.

MERFISH mouse dataset

A comparative study, in collaboration with Vizgen, Inc. and UC San Francisco, of MERFISH spatial transcriptomics in mouse liver and kidney with bulk and single-cell RNA sequencing data from Tabula Muris Senis.

dexp

dexp is a napari, CuPy, Zarr, and DASK based library for managing, processing and visualizing light-sheet microscopy datasets.

microDL

Software that allows the user to design, train, and evaluate U-Net models using YAML config files.

recOrder

A package that offers a comprehensive pipeline, command line interface, and napari plugin for quantitative label-free microscopy.

WaveOrder

Software to measure intrinsic order with wave optical reconstructions of density and anisotropy.

Aydin: User-friendly, feature-rich, fast image denoising tool for all

Aydin is a user-friendly, feature-rich, and fast image denoising tool that provides a number of self-supervised, auto-tuned, and unsupervised image denoising algorithms.

Human Lung Cell Atlas

Provides the molecular foundation for investigating how lung cell identities, functions, and interactions are achieved in development and tissue engineering and altered in disease and evolution.

Fly Cell Atlas

The Fly Cell Atlas brings together Drosophila researchers interested in single-cell genomics, transcriptomics, and epigenomics, to build comprehensive cell atlases during different developmental stages and disease models.

Chan Zuckerberg GEN EPI

Secure, cloud-based platform with no-code genomic epidemiology analysis platform for public health.

DASHit

DASHit is a collection of software for the automated design and evaluation of Cas9 guide RNAs for DASH experiments.

CrispyCrunch

CrispyCrunch is a tool for defining batches of CRISPR edits and analyzing their basic effects.

Metagenomic sequencing: Introduction and lab setup

Part 1 of the Metagenomic Sequencing training from the Rapid Response Team.

Metagenomic sequencing: Study design and sample preparation

Part 2 of the Metagenomic Sequencing training from the Rapid Response Team. Provides overview of study design and best practices for xNA extraction.

Metagenomic sequencing: Introduction to Illumina sequencing and data analysis for mNGS using IDseq

Part 3 of the Metagenomic Sequencing training from the Rapid Response Team. Provides an introduction to Illumina and an overview of library prep, sequencing, data analysis, and Pathogen ID.

Metagenomic sequencing: Library preparation for mNGS

Part 4 of the Metagenomic Sequencing training from the Rapid Response Team. In-depth guide on the process of library preparation.

Metagenomic sequencing: Loading the sequencer – iSeq loading guide

Part 5 of the Metagenomic Sequencing training from the Rapid Response Team. A step-by-step guide on loading the iSeq 100.

Metagenomic sequencing: Loading the sequencer – MiSeq loading guide

Part 6 of 6 of the Metagenomic Sequencing training from the Rapid Response Team. A step-by-step guide to setting up and loading the Illumina MiSeq.

Enrichment/depletion methods for sequencing: FLASH protocol

Finding Low Abundance Sequences by Hybridization (FLASH) Protocol developed at CZ Biohub.

Enrichment/depletion methods for sequencing: FLASH publication

Official publication of the Finding Low Abundance Sequences by Hybridization (FLASH) protocol developed at CZ Biohub.

How to make your own SPRI beads

Overview and training guide on homemade Solid Phase Reverse Immobilization (SPRI) beads.

Sequencing SARS-CoV-2 for public health laboratories

CZ Biohub Rapid Response Team's handbook for public health labs on sequencing SARS-CoV2.

Scaling sequencing

Instructions from CZ Biohub Rapid Response team on increasing sample throughput for sequencing, levels of scaling, and equipment options for each level.

Metagenomic next-generation sequencing (mNGS) protocol

A centralized location for protocols used for the mNGS training for the Gates Grand Challenges Explorations Grants. Contains guidelines for best practices that are subject to change.

SARS-CoV-2 ARTIC sequencing using Illumina; library prep protocol V.4

Most up-to-date version of the protocol for experiment investigating the effect of fragmentation time on the genome recovery of SARS-CoV-2 from COVID-19-positive patient samples.

Tools

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