April 15, 2019  |  CITE-seq, Education

How-to: Analyze CITE-seq Data in Cytobank

CITE-seq, or Cellular Indexing of Transcriptomes and Epitopes by sequencing [1], is one of the latest innovations for studying single-cell biology. It enables researchers to simultaneously capture RNA and surface protein expression on the same cells with next generation sequencing technology. Scientists can correlate the two data types and identify biomarkers and better characterize cell phenotypes [2]. The normalization and comparison of the two data types, however, do present data analysis challenges. At Cytobank, we want to make CITE-seq data analysis easier and help you discover more.

Here’s an approach that utilizes the Cytobank platform and should help you effectively analyze your multi-omic CITE-seq data. More »

March 15, 2019  |  Education, FlowSOM, viSNE

Beginner’s guide to FlowSOM: Profiling the innate immune response to viral infection

FlowSOM detailChikungunya virus is transmitted to humans in tropical regions through the bite of a mosquito carrying the virus. Pediatric populations are most at risk for developing acute illness of fever, rash, and joint pain, often followed chronic, debilitating arthritis. With no available vaccine or effective anti-viral treatment, a comprehensive immunophenotyping study was performed by Michlmayr et. al. on PBMCs of 42 children during acute and convalescent phases of infection, to better understand the innate anti-viral immune response.

Using 35-parameter CyTOF data available on ImmPort (SDY1288), we applied Cytobank’s machine learning tools viSNE followed by FlowSOM to simplify visualization, then cluster cells and identify which clusters were altered during acute infection. More »

November 30, 2018  |  Announcements, Education, FlowSOM, Release Notes

Announcing: Cytobank 7.0 with FlowSOM

We are delighted to introduce our latest version of Cytobank.

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Included in this release are many performance and interface improvements, as well as a notable new addition to our repertoire of integrated algorithms. As we continue to evolve and improve our platform in response to your needs and feedback, we also look to leaders in our field to expand our capabilities and bring high-level developments in bioinformatics to you in an approachable and easy-to-use way.
In this spirit, we introduce
FlowSOM in Cytobank More »

Webinar Recording: Explore Hidden Cell Populations with cytoclustR

TregsviSNEShahramOur recent Webinar with Dr. Shahram Kordasti and Bioinformatician Thanos Mourikis explored cytoclustR, a new tool they developed with the Cytobank API.

Dr. Kordasti began by reviewing how he set up his experiment pipeline to best identify Treg populations, as outlined in his article featured on the cover of Blood Journal.

Thanos followed with a step-by-step tutorial on how to use cytoclustR with SpadeTreeShahramSPADE in Cytobank to distinguish and report on hidden cell populations that might otherwise go unnoticed with manual gating strategies.

cyobankarrow40x40Check out the recording on our YouTube channel

June 28, 2018  |  API, Education, SPADE, viSNE, Webinars

July Webinar:
Explore Hidden Cell Populations with cytoClustR and the Cytobank API

Best Practices for Adopting Clustering Pipelines in Place ofSPADE Tree Kordasti Manual Gating

Join us Wednesday, July 18 at 9:00 AM PDT for our next free webinar. Learn how Physician Scientist, Dr. Shahram Kordasti of King’s College London and Bioinformatician Thanos Mourikis of Cancer Research UK (CRUK) collaborated to build cytoClustR, a tool you can use with Cytobank’s machine learning algorithms to identify cell subsets in order to help make discoveries in the clinic.

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More »

Top Trends, Presentations, and Takeaways from CYTO 2018

CYTO, the International Society for the Advancement of Cytometry (ISAC)’s annual meeting wrapped up earlier this month in the exciting city of Prague, Czech Republic. As the premier meeting for showcasing the state of the art and science of cytometry, CYTO and its members revealed no small number of exciting developments in cytometry and beyond. We’re just now getting around to sharing all we saw and heard at the meeting. Some of our favorite presentations and observations include: More »

May 25, 2018  |  Education, Events, viSNE, Webinars

Webinar Recap: Advanced viSNE (t-SNE) Review

Untitled-1Nearly 500 scientists registered for our latest data analysis webinar. Cytobank Application Scientist Geoff Kraker took us on a tour of recently added features like setting the seed (for replicating results), configuring display gate labels, and more. If you missed it, not to worry. The recording is now available online.

cyobankarrow40x40View our latest webinars on the Cytobank YouTube channel

Following the demo, Geoff fielded many great live questions from the viewers. Here are some of our favorites: More »

April 30, 2018  |  Education, Events, viSNE, Webinars

May Webinar: New Developments in viSNE Presented by Geoff Kraker

If you missed the webinar, click here to view the recording on our YouTube Channel.

Join us for our free Webinar May 17, 2018 9:00 AM PDT/ 16:00 GMT

In our previous and popular webinars featuring viSNE, hundreds have logged on to watch as scientists showed us how they used viSNE to make discoveries in the clinic and build comprehensive data analysis pipelines for their high parameter data.

With recent improvements released on Cytobank, it’s a great time to gather and review viSNE best practices, to dive deeper into how you can now explore your data more efficiently with viSNE, and how you can extend viSNE’s capabilities by integrating with other analysis approaches, including basic analysis and more advanced machine learning algorithms.visne_display_gates More »