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
MIDAS
Metagenomic Intra-Species Diversity Analysis (MIDAS)
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/MIDAS
Metagenomic Intra-Species Diversity Analysis (MIDAS)
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/excellxgene
czbiohub-sf/yogo
The "you only glance once" object detection model
czbiohub-sf/AIRRscape
R Shiny tool to interactively visualize and analyze antibody repertoires
czbiohub-sf/coPylot
coPylot - microscope control
czbiohub-sf/shrimPy
shrimPy: Smart High-throughput Robust Imaging & Measurement in Python
czbiohub-sf/protoSpaceJAM
CRISPR knock-in design at scale
czbiohub-sf/covid19-transcriptomics-pathogenesis-diagnostics-results
czbiohub-sf/crispycrunch
Web app for CRISPR experiment setup and analysis
czbiohub-sf/2021-opencell-figures
Public read-only repo for code and data related to the 2021 OpenCell preprint
czbiohub-sf/czb-ui
CZ Biohub's higher level components made with CZI's Science Design System Component Library.
czbiohub-sf/EpiGen-COVID19
Using both phylogenetic and time-series data from the COVID19 pandemic to estimate number of missing infections and predict forward epidemic trajectory.
czbiohub-sf/Organelle_IP_analyses_and_figures
Jupyter notebooks for analysis and figures related to the native organelle IP paper
czbiohub-sf/zebrahub_analysis
Analysis of single-cell single-embryo RNA seq data from the zebrafish developmental atlas Zebrahub.
czbiohub-sf/bcell_pipeline
Immcantation B-cell Repertoire Sequencing Pipeline adapted for Reflow
czbiohub-sf/napari-iohub
OME-Zarr viewer for napari with iohub as the I/O backend
czbiohub-sf/GenoPrimer
Automated primer design for genotyping CRISPR edited cells
czbiohub-sf/maca
Command line utilities for RNA-sequencing data
czbiohub-sf/zebrahub-multiome-analysis
A repository for scripts and notebooks to process and analyze single-cell Multiome datasets from early zebrafish embryos (zebrahub)
czbiohub-sf/comparison-RNAVelo
Comparison of single-cell RNA Velocity methods in developmental contexts
czbiohub-sf/DeepGenotype
Calculate the outcome genotype frequencies in CRISPR genome editing experiments using deep sequencing reads.
czbiohub-sf/napari-plugins-docker
Build a Napari image with common plugins
czbiohub-sf/special_ops_crispr_tools
Computational tools for identifying CRISPR targets and offtargets.
czbiohub-sf/markov-bridges
czbiohub-sf/proteinxlocation
An interactive explorer for single-cell transcriptomics data
czbiohub-sf/protoSpaceJAM-portal
Webserver allowing non-bioinformaticians to easily run protospaceJAM.
czbiohub-sf/random-walk-epidemic-model
A random walk epidemic model.
czbiohub-sf/sc2-guide-InSilicoSCR
InSilico off-target screening for SC2 guides.