Python  Library

Python Library


Cellxgene | An Interactive Data Explorer for Single-cell Datasets

an interactive explorer for single-cell transcriptomics data

cellxgene Desktop (pronounced "cell-by-gene") is an interactive data explorer for single-cell datasets, such as those coming from the Human Cell Atlas. Leveraging modern web development techniques to enable fast visualizations of at least 1 million cells, we hope to enable biologists and computational researchers to explore their data.

Whether you need to visualize one thousand cells or one million, cellxgene Desktop helps you gain insight into your single-cell data.

Getting started

The comprehensive guide to cellxgene Desktop

The cellxgene documentation is your one-stop-shop for information about cellxgene Desktop! You may be particularly interested in:

Quick start

To install cellxgene Desktop you need Python 3.6+. We recommend installing cellxgene Desktop into a conda or virtual environment.

Install the package.

pip install cellxgene

Launch cellxgene Desktop with an example anndata file

cellxgene launch

To explore more datasets already formatted for cellxgene Desktop, check out the Demo data or see Preparing your data to learn more about formatting your own data for cellxgene Desktop.

Supported browsers

cellxgene Desktop currently supports the following browsers:

  • Google Chrome 61+
  • Edge 15+
  • Firefox 60+

Please file an issue if you would like us to add support for an unsupported browser.

Finding help

We'd love to hear from you! For questions, suggestions, or accolades, join the #cellxgene-users channel on the CZI Science Slack and say "hi!".

For any errors, report bugs on Github.

Developing with cellxgene Desktop


We warmly welcome contributions from the community! Please see our contributing guide and don't hesitate to open an issue or send a pull request to improve cellxgene Desktop. Please see the dev_docs for pull request suggestions, unit test details, local documentation preview, and other development specifics.

This project adheres to the Contributor Covenant code of conduct. By participating, you are expected to uphold this code. Please report unacceptable behavior to


This project was started with the sole goal of empowering the scientific community to explore and understand their data. As such, we encourage other scientific tool builders in academia or industry to adopt the patterns, tools, and code from this project. All code is freely available for reuse under the MIT license.

Before extending cellxgene, we encourage you to reach out to us with ideas or questions. It might be possible that an extension could be directly contributed, which would make it available for a wider audience, or that it's on our roadmap and under active development.

See the cellxgene extensions section of our documentation for examples of community use and cellxgene extensions.


If you believe you have found a security issue, we would appreciate notification. Please send email to


We've been heavily inspired by several other related single-cell visualization projects, including the UCSC Cell Browser, Cytoscape, Xena, ASAP, GenePattern, and many others. We hope to explore collaborations where useful as this community works together on improving interactive visualization for single-cell data.

We were inspired by Mike Bostock and the crossfilter team for the design of our filtering implementation.

We have been working closely with the scanpy team to integrate with their awesome analysis tools. Special thanks to Alex Wolf, Fabian Theis, and the rest of the team for their help during development and for providing an example dataset.

We are eager to explore integrations with other computational backends such as Seurat or Bioconductor

Download Details:
Author: chanzuckerberg
Source Code:
License: MIT license


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Cellxgene | An Interactive Data Explorer for Single-cell Datasets
 iOS App Dev

iOS App Dev


Your Data Architecture: Simple Best Practices for Your Data Strategy

If you accumulate data on which you base your decision-making as an organization, you should probably think about your data architecture and possible best practices.

If you accumulate data on which you base your decision-making as an organization, you most probably need to think about your data architecture and consider possible best practices. Gaining a competitive edge, remaining customer-centric to the greatest extent possible, and streamlining processes to get on-the-button outcomes can all be traced back to an organization’s capacity to build a future-ready data architecture.

In what follows, we offer a short overview of the overarching capabilities of data architecture. These include user-centricity, elasticity, robustness, and the capacity to ensure the seamless flow of data at all times. Added to these are automation enablement, plus security and data governance considerations. These points from our checklist for what we perceive to be an anticipatory analytics ecosystem.

#big data #data science #big data analytics #data analysis #data architecture #data transformation #data platform #data strategy #cloud data platform #data acquisition

Gerhard  Brink

Gerhard Brink


Getting Started With Data Lakes

Frameworks for Efficient Enterprise Analytics

The opportunities big data offers also come with very real challenges that many organizations are facing today. Often, it’s finding the most cost-effective, scalable way to store and process boundless volumes of data in multiple formats that come from a growing number of sources. Then organizations need the analytical capabilities and flexibility to turn this data into insights that can meet their specific business objectives.

This Refcard dives into how a data lake helps tackle these challenges at both ends — from its enhanced architecture that’s designed for efficient data ingestion, storage, and management to its advanced analytics functionality and performance flexibility. You’ll also explore key benefits and common use cases.


As technology continues to evolve with new data sources, such as IoT sensors and social media churning out large volumes of data, there has never been a better time to discuss the possibilities and challenges of managing such data for varying analytical insights. In this Refcard, we dig deep into how data lakes solve the problem of storing and processing enormous amounts of data. While doing so, we also explore the benefits of data lakes, their use cases, and how they differ from data warehouses (DWHs).

This is a preview of the Getting Started With Data Lakes Refcard. To read the entire Refcard, please download the PDF from the link above.

#big data #data analytics #data analysis #business analytics #data warehouse #data storage #data lake #data lake architecture #data lake governance #data lake management

Uriah  Dietrich

Uriah Dietrich


What Is ETLT? Merging the Best of ETL and ELT Into a Single ETLT Data Integration Strategy

Data integration solutions typically advocate that one approach – either ETL or ELT – is better than the other. In reality, both ETL (extract, transform, load) and ELT (extract, load, transform) serve indispensable roles in the data integration space:

  • ETL is valuable when it comes to data quality, data security, and data compliance. It can also save money on data warehousing costs. However, ETL is slow when ingesting unstructured data, and it can lack flexibility.
  • ELT is fast when ingesting large amounts of raw, unstructured data. It also brings flexibility to your data integration and data analytics strategies. However, ELT sacrifices data quality, security, and compliance in many cases.

Because ETL and ELT present different strengths and weaknesses, many organizations are using a hybrid “ETLT” approach to get the best of both worlds. In this guide, we’ll help you understand the “why, what, and how” of ETLT, so you can determine if it’s right for your use-case.

#data science #data #data security #data integration #etl #data warehouse #data breach #elt #bid data

Cyrus  Kreiger

Cyrus Kreiger


How Has COVID-19 Impacted Data Science?

The COVID-19 pandemic disrupted supply chains and brought economies around the world to a standstill. In turn, businesses need access to accurate, timely data more than ever before. As a result, the demand for data analytics is skyrocketing as businesses try to navigate an uncertain future. However, the sudden surge in demand comes with its own set of challenges.

Here is how the COVID-19 pandemic is affecting the data industry and how enterprises can prepare for the data challenges to come in 2021 and beyond.

#big data #data #data analysis #data security #data integration #etl #data warehouse #data breach #elt

Macey  Kling

Macey Kling


Applications Of Data Science On 3D Imagery Data

CVDC 2020, the Computer Vision conference of the year, is scheduled for 13th and 14th of August to bring together the leading experts on Computer Vision from around the world. Organised by the Association of Data Scientists (ADaSCi), the premier global professional body of data science and machine learning professionals, it is a first-of-its-kind virtual conference on Computer Vision.

The second day of the conference started with quite an informative talk on the current pandemic situation. Speaking of talks, the second session “Application of Data Science Algorithms on 3D Imagery Data” was presented by Ramana M, who is the Principal Data Scientist in Analytics at Cyient Ltd.

Ramana talked about one of the most important assets of organisations, data and how the digital world is moving from using 2D data to 3D data for highly accurate information along with realistic user experiences.

The agenda of the talk included an introduction to 3D data, its applications and case studies, 3D data alignment, 3D data for object detection and two general case studies, which are-

  • Industrial metrology for quality assurance.
  • 3d object detection and its volumetric analysis.

This talk discussed the recent advances in 3D data processing, feature extraction methods, object type detection, object segmentation, and object measurements in different body cross-sections. It also covered the 3D imagery concepts, the various algorithms for faster data processing on the GPU environment, and the application of deep learning techniques for object detection and segmentation.

#developers corner #3d data #3d data alignment #applications of data science on 3d imagery data #computer vision #cvdc 2020 #deep learning techniques for 3d data #mesh data #point cloud data #uav data