Discover czbiohub-sf/bucketbase Open Source project

Code and annotations for the Tabula Muris single-cell transcriptomic dataset.

313

tabula-muris

This is the repository that contains the analysis of the lung adenocarcinoma single cell dataset

183

scell_lung_adenocarcinoma

xi correlation method adapted for python

142

xicor

tabula-muris-senis

learn-bioinformatics

List of resources for learning bioinformatics, from beginner to advanced

A tool for fast and accurate summarizing of variant calling format (VCF) files

cerebra

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

tabula-sapiens

Metagenomic Intra-Species Diversity Analysis (MIDAS)

MIDAS

Pythonic and parallelizable I/O for N-dimensional imaging data with OME metadata

iohub

Bioinformatics pipeline for SARS-CoV-2 sequencing at CZ Biohub

sc2-illumina-pipeline

Examples analyses using the single-cell RNA-seq data from mouse cell atlases

tabula-muris-vignettes

Makefile

orpheum

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

Single-cell identity definition using random forest modelling and recursive feature elimination

scRFE

R Shiny tool to interactively visualize and analyze antibody repertoires

AIRRscape

excellxgene

JavaScript

utilities

A collection of scripts for common data management and processing tasks

mspipelines

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

california-mosquito-study

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

shrimPy

coPylot - microscope control

coPylot

Dashboard for visualizing sequencing QC of plates from a single cell RNA-seq project

singlecell-dash

Automatically create CRISPR guides for DASH ✂️

dashit

flash

Web app for CRISPR experiment setup and analysis

crispycrunch

Spid.jl

Julia

covid19-transcriptomics-pathogenesis-diagnostics-results

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

scrnaseq-for-the-99-percent

An installer for in situ transcriptomics image processing tools

InSituToolkit

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

pomelo

nf-predictorthologs

*de novo* orthologous gene predictions from bam + bed or fasta/fastq data

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

EpiGen-COVID19

opencell-portal-pub

Public read-only repo for the OpenCell database and web app

An interactive database for virus-centric CRISPR screens

v-host-factor-db

how to make the most out of cellxgene

cellxgene-training

napari-mosquito-bb-annotations

Napari plugin for bounding box annotations

notes on frameshifts and other genbank related notes

covidtracker_notes

bcell_pipeline

Immcantation B-cell Repertoire Sequencing Pipeline adapted for Reflow

czb-ui

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

TypeScript

CovidTissueAtlas

UCSF Covid Tissue Atlas

MAGeCK analysis automated by Nextflow

CRISPRflow

human_melanocytes

Single cell RNA-seq of human melanocytes

A library to simulate single-cell data

simscity

Calibrate and compare methods for denoising single-cell RNA-seq data

molecular-cross-validation

Realtime quality control for mass spectrometry data acquisition

MS-AutoQC

Tools for crowd-sourced annotation of FISH images

instapipeline

Repository for Introduction to Data Visualization in Python for Interns 2021

interns-2021-dataviz

Command line utilities for RNA-sequencing data

maca

nf-epigen

Monorepo for Datahub projects

datahub

Rust

celltype_annotation_tutorial

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

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

zebrahub_analysis

Automated primer design for genotyping CRISPR edited cells

GenoPrimer

A Napari Plugin for annotating open-cell data

InfectedCellMicroscopyAnnotator

epidemiology_flux_model

Average Nucleotide Identity Pairwise Distance Computation For Microbiome

pairani

Dockerfile

ncov-modeling-jc

hovernet_he

realtime-tracking-covid19

realtime-covid19-tracking

covidhub-pub

Pyseus: Perseus in Python

pyseus

Public repo for OpenCell-related microscopy automation software

2021-opencell-microscopy-automation

nf-simulaternaseq

Simulate RNA-seq reads

ds-infected-cell-summer

Software for hardware systems built in response to emerging needs

BioE-Bartender

C++

automated-protein-purifier

Contains Python application and czpurifier package for automated protein purification

Image processing software for the Label-free malaria imaging project.

UVScope-control

UVScope control software

MATLAB

Label-Free-Malaria

MATLAB

2021-opencell-figures

Public read-only repo for code and data related to the 2021 OpenCell preprint

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

DeepGenotype

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

2023-facs-automation-pub

Ultra Low Cost Optical Density Meter Repository

ULC-OD-Meter

C++

napari-iohub

OME-Zarr viewer for napari with iohub as the I/O backend

This workflow will find unspliced coding sequences from bams.

nf-unsplicedcds