Discover czbiohub-sf/MIDAS 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

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

coPylot - microscope control

coPylot

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

singlecell-dash

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

shrimPy

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

Compare orthologous genes across species using k-mer similarity

nf-ortholog

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

bucketbase

Single cell RNA-seq of human melanocytes

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

Stabilize x-y shifts in long time series videos. This is a wrapper around the ImageJ plugin "ImageStabilizer" that enables the jar to be run from command line with conventional flags

ImageStabilizer

Java

zebrahub_analysis

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

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++

GenoPrimer

Automated primer design for genotyping CRISPR edited cells

Contains Python application and czpurifier package for automated protein purification

automated-protein-purifier

dotblotr: a microarray image processing package

dotblotr

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

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