Chan Zuckerberg Biohub (@czbiohub-sf)
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czbiohub-sf

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Top repositories

1

noise2self

A framework for blind denoising with self-supervision.
Jupyter Notebook
313
star
2

tabula-muris

Code and annotations for the Tabula Muris single-cell transcriptomic dataset.
HTML
183
star
3

scell_lung_adenocarcinoma

This is the repository that contains the analysis of the lung adenocarcinoma single cell dataset
HTML
142
star
4

xicor

xi correlation method adapted for python
Jupyter Notebook
126
star
5

tabula-muris-senis

Tabula Muris Senis
Jupyter Notebook
96
star
6

learn-bioinformatics

List of resources for learning bioinformatics, from beginner to advanced
Jupyter Notebook
87
star
7

cerebra

A tool for fast and accurate summarizing of variant calling format (VCF) files
Python
60
star
8

tabula-sapiens

Single Cell Transcriptomics of 25 Human Organs to Create a Tabula Sapiens
Jupyter Notebook
38
star
9

MIDAS

Metagenomic Intra-Species Diversity Analysis (MIDAS)
Python
35
star
10

iohub

Pythonic and parallelizable I/O for N-dimensional imaging data with OME metadata
Python
27
star
11

sc2-illumina-pipeline

Bioinformatics pipeline for SARS-CoV-2 sequencing at CZ Biohub
Nextflow
25
star
12

tabula-muris-vignettes

Examples analyses using the single-cell RNA-seq data from mouse cell atlases
Makefile
22
star
13

orpheum

Orpheum (Previously called and published under sencha) is a Python package for directly translating RNA-seq reads into coding protein sequence.
Python
18
star
14

scRFE

Single-cell identity definition using random forest modelling and recursive feature elimination
Jupyter Notebook
12
star
15

AIRRscape

R Shiny tool to interactively visualize and analyze antibody repertoires
R
10
star
16

excellxgene

JavaScript
10
star
17

utilities

A collection of scripts for common data management and processing tasks
Nextflow
9
star
18

mspipelines

Python
8
star
19

california-mosquito-study

Source code and data supporting our eLife manuscript on single mosquito sequencing (https://elifesciences.org/articles/68353)
Jupyter Notebook
8
star
20

shrimPy

shrimPy: Smart High-throughput Robust Imaging & Measurement in Python
Python
8
star
21

coPylot

coPylot - microscope control
Python
8
star
22

singlecell-dash

Dashboard for visualizing sequencing QC of plates from a single cell RNA-seq project
Python
7
star
23

dashit

Automatically create CRISPR guides for DASH ✂️
Python
6
star
24

flash

Python
6
star
25

crispycrunch

Web app for CRISPR experiment setup and analysis
Python
6
star
26

Spid.jl

Julia
5
star
27

covid19-transcriptomics-pathogenesis-diagnostics-results

Jupyter Notebook
5
star
28

scrnaseq-for-the-99-percent

Code accompanying the paper titled, "Single-cell transcriptomics for the 99.9% of species without reference genomes" by Botvinnik et al, 2021
Jupyter Notebook
5
star
29

InSituToolkit

An installer for in situ transcriptomics image processing tools
Python
4
star
30

pomelo

A novel bioinformatic approach for identifying metabolic vulnerabilities of pathogens to Inform host-directed therapeutics
R
4
star
31

nf-predictorthologs

*de novo* orthologous gene predictions from bam + bed or fasta/fastq data
Nextflow
4
star
32

EpiGen-COVID19

Using both phylogenetic and time-series data from the COVID19 pandemic to estimate number of missing infections and predict forward epidemic trajectory.
R
4
star
33

opencell-portal-pub

Public read-only repo for the OpenCell database and web app
Jupyter Notebook
3
star
34

v-host-factor-db

An interactive database for virus-centric CRISPR screens
HTML
3
star
35

cellxgene-training

how to make the most out of cellxgene
3
star
36

napari-mosquito-bb-annotations

Napari plugin for bounding box annotations
Python
3
star
37

covidtracker_notes

notes on frameshifts and other genbank related notes
3
star
38

bcell_pipeline

Immcantation B-cell Repertoire Sequencing Pipeline adapted for Reflow
R
3
star
39

czb-ui

CZ Biohub's higher level components made with CZI's Science Design System Component Library.
TypeScript
3
star
40

CovidTissueAtlas

UCSF Covid Tissue Atlas
Jupyter Notebook
2
star
41

CRISPRflow

MAGeCK analysis automated by Nextflow
R
2
star
42

bucketbase

Jupyter Notebook
2
star
43

human_melanocytes

Single cell RNA-seq of human melanocytes
Jupyter Notebook
2
star
44

simscity

A library to simulate single-cell data
Python
2
star
45

molecular-cross-validation

Calibrate and compare methods for denoising single-cell RNA-seq data
Python
2
star
46

MS-AutoQC

Realtime quality control for mass spectrometry data acquisition
Python
2
star
47

instapipeline

Tools for crowd-sourced annotation of FISH images
Jupyter Notebook
2
star
48

interns-2021-dataviz

Repository for Introduction to Data Visualization in Python for Interns 2021
Jupyter Notebook
2
star
49

maca

Command line utilities for RNA-sequencing data
Python
2
star
50

nf-epigen

Jupyter Notebook
2
star
51

datahub

Monorepo for Datahub projects
Rust
2
star
52

celltype_annotation_tutorial

A repository for notebooks, figures, and utilities for cell-type annotation tutorial manuscript using CZ CELLxGENE ecosystem
Jupyter Notebook
2
star
53

zebrahub_analysis

Analysis of single-cell single-embryo RNA seq data from the zebrafish developmental atlas Zebrahub.
Jupyter Notebook
2
star
54

GenoPrimer

Automated primer design for genotyping CRISPR edited cells
Python
1
star
55

InfectedCellMicroscopyAnnotator

A Napari Plugin for annotating open-cell data
Python
1
star
56

epidemiology_flux_model

Jupyter Notebook
1
star
57

pairani

Average Nucleotide Identity Pairwise Distance Computation For Microbiome
Dockerfile
1
star
58

ncov-modeling-jc

HTML
1
star
59

hovernet_he

Python
1
star
60

realtime-covid19-tracking

realtime-tracking-covid19
1
star
61

covidhub-pub

Jupyter Notebook
1
star
62

pyseus

Pyseus: Perseus in Python
Python
1
star
63

2021-opencell-microscopy-automation

Public repo for OpenCell-related microscopy automation software
Jupyter Notebook
1
star
64

nf-simulaternaseq

Simulate RNA-seq reads
Nextflow
1
star
65

ds-infected-cell-summer

Jupyter Notebook
1
star
66

BioE-Bartender

Software for hardware systems built in response to emerging needs
C++
1
star
67

automated-protein-purifier

Contains Python application and czpurifier package for automated protein purification
Python
1
star
68

UVScope-control

UVScope control software
MATLAB
1
star
69

Label-Free-Malaria

Image processing software for the Label-free malaria imaging project.
MATLAB
1
star
70

2021-opencell-figures

Public read-only repo for code and data related to the 2021 OpenCell preprint
Jupyter Notebook
1
star
71

DeepGenotype

Calculate the outcome genotype frequencies in CRISPR genome editing experiments using deep sequencing reads.
HTML
1
star
72

2023-facs-automation-pub

Python libraries for automating cell sorting with the Sony SH800S GUI.
Python
1
star
73

ULC-OD-Meter

Ultra Low Cost Optical Density Meter Repository
C++
1
star
74

napari-iohub

OME-Zarr viewer for napari with iohub as the I/O backend
Python
1
star
75

nf-unsplicedcds

This workflow will find unspliced coding sequences from bams.
Nextflow
1
star