Pinned Repositories
cerebra
A tool for fast and accurate summarizing of variant calling format (VCF) files
learn-bioinformatics
List of resources for learning bioinformatics, from beginner to advanced
MIDAS2
Metagenomic Intra-Species Diversity Analysis 2
noise2self
A framework for blind denoising with self-supervision.
scell_lung_adenocarcinoma
This is the repository that contains the analysis of the lung adenocarcinoma single cell dataset
tabula-muris
Code and annotations for the Tabula Muris single-cell transcriptomic dataset.
tabula-muris-senis
Tabula Muris Senis
tabula-sapiens
Single Cell Transcriptomics of 25 Human Organs to Create a Tabula Sapiens
xicor
xi correlation method adapted for python
zebrahub_analysis
Analysis of single-cell single-embryo RNA seq data from the zebrafish developmental atlas Zebrahub.
Chan Zuckerberg Biohub San Francisco's Repositories
czbiohub-sf/tabula-sapiens
Single Cell Transcriptomics of 25 Human Organs to Create a Tabula Sapiens
czbiohub-sf/MIDAS2
Metagenomic Intra-Species Diversity Analysis 2
czbiohub-sf/iohub
Pythonic and parallelizable I/O for N-dimensional imaging data with OME metadata
czbiohub-sf/Rapid-QC-MS
Realtime quality control for mass spectrometry data acquisition
czbiohub-sf/AIRRscape
R Shiny tool to interactively visualize and analyze antibody repertoires
czbiohub-sf/excellxgene
czbiohub-sf/utilities
A collection of scripts for common data management and processing tasks
czbiohub-sf/coPylot
coPylot - microscope control
czbiohub-sf/yogo
The "you only glance once" object detection model
czbiohub-sf/shrimPy
shrimPy: Smart High-throughput Robust Imaging & Measurement in Python
czbiohub-sf/czb-ui
CZ Biohub's higher level components made with CZI's Science Design System Component Library.
czbiohub-sf/protoSpaceJAM
CRISPR knock-in design at scale
czbiohub-sf/pomelo
A novel bioinformatic approach for identifying metabolic vulnerabilities of pathogens to Inform host-directed therapeutics
czbiohub-sf/luminoth
Object detection using Faster RCNN, SSD
czbiohub-sf/Organelle_IP_analyses_and_figures
Jupyter notebooks for analysis and figures related to the native organelle IP paper
czbiohub-sf/celltype_annotation_tutorial
A repository for notebooks, figures, and utilities for cell-type annotation tutorial manuscript using CZ CELLxGENE ecosystem
czbiohub-sf/CovidTissueAtlas
UCSF Covid Tissue Atlas
czbiohub-sf/CRISPRflow
MAGeCK analysis automated by Nextflow
czbiohub-sf/GenoPrimer
Automated primer design for genotyping CRISPR edited cells
czbiohub-sf/zebrahub_analysis
Analysis of single-cell single-embryo RNA seq data from the zebrafish developmental atlas Zebrahub.
czbiohub-sf/automated-protein-purifier
Contains Python application and czpurifier package for automated protein purification
czbiohub-sf/portable-luminometer
Software and electronics for the portable SiPM luminometer.
czbiohub-sf/PyMotors
A collection of motor classes and utilities in Python 3.
czbiohub-sf/special_ops_crispr_tools
Computational tools for identifying CRISPR targets and offtargets.
czbiohub-sf/.github
Organization-level readme and documentation
czbiohub-sf/czbiohub_openxdmod
This is an openxdmod container for the bruno super computer @ biohub sf
czbiohub-sf/DeepGenotype
Calculate the outcome genotype frequencies in CRISPR genome editing experiments using deep sequencing reads.
czbiohub-sf/markov-bridges
czbiohub-sf/metaquery
czbiohub-sf/rapid-response-prism
Phylogenetic analysis of various respiratory viruses captured during the PRISM study in Uganda.