Chan Zuckerberg Biohub San Francisco

tabula-muris-senis

Tabula Muris Senis

tabula-sapiens

Single Cell Transcriptomics of 25 Human Organs to Create a Tabula Sapiens

MIDAS2

Metagenomic Intra-Species Diversity Analysis 2

iohub

N-dimensional bioimaging data I/O with OME metadata in Python

Rapid-QC-MS

Realtime quality control for mass spectrometry data acquisition

AIRRscape

R Shiny tool to interactively visualize and analyze antibody repertoires

excellxgene

utilities

A collection of scripts for common data management and processing tasks

coPylot

coPylot - microscope control

czb-ui

CZ Biohub's higher level components made with CZI's Science Design System Component Library.

protoSpaceJAM

CRISPR knock-in design at scale

shrimPy

shrimPy: Smart High-throughput Robust Imaging & Measurement in Python

pomelo

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

luminoth

Object detection using Faster RCNN, SSD

Organelle_IP_analyses_and_figures

Jupyter notebooks for analysis and figures related to the native organelle IP paper

celltype_annotation_tutorial

A repository for notebooks, figures, and utilities for cell-type annotation tutorial manuscript using CZ CELLxGENE ecosystem

CovidTissueAtlas

UCSF Covid Tissue Atlas

CRISPRflow

MAGeCK analysis automated by Nextflow

GenoPrimer

Automated primer design for genotyping CRISPR edited cells

zebrahub_analysis

Analysis of single-cell single-embryo RNA seq data from the zebrafish developmental atlas Zebrahub.

2023-facs-automation-pub

Python libraries for automating cell sorting with the Sony SH800S GUI.

automated-protein-purifier

Contains Python application and czpurifier package for automated protein purification

portable-luminometer

Software and electronics for the portable SiPM luminometer.

PyMotors

A collection of motor classes and utilities in Python 3.

special_ops_crispr_tools

Computational tools for identifying CRISPR targets and offtargets.

.github

Organization-level readme and documentation

DeepGenotype

Calculate the outcome genotype frequencies in CRISPR genome editing experiments using deep sequencing reads.

markov-bridges

metaquery

rapid-response-prism

Phylogenetic analysis of various respiratory viruses captured during the PRISM study in Uganda.