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Cloud Based Single Cell Informatics

Single Cell Informatics

Overview of Products

Qognit has developed a cloud based software platform that has been specifically designed to meet the challenges of high-dimensional, large scale single cell data. Our platform is highly performant and feature rich with built-in intelligence for single cell data management and analysis. Each of our products, built on this foundation, focus on specific assay formats (e.g. cytometry), providing the end-user with highly interactive interfaces to perform end-to-end workflows ranging from designing experiments to managing data and performing analysis. All of our products are designed to integrate with other informatics systems with centralization of data and analysis and can scale with your growing data needs. Current product offerings include Ryvett for cytometry, Celsight for single cell multi-omics data, and PlexScope for multiplex beads assays.



The most comprehensive software platform for design, management and analysis of Cytometry data.

Ryvett is a modular, cloud-based software platform with extensive functionality to support end-to-end cytometry workflows and analysis. Deployed in a single-tenant or multi-tenant configuration, Ryvett is architected and built to be 21 CFR Part 11 compliant with access control, traceability, and audit capabilities. Ryvett’s modules can be deployed independently or together to meet your needs:

  • Design Module: Collaborate, design, and plan experiments with automated metadata entry and export acquisition ready experiment files with harmonized annotations across experiments
  • Analysis Module: Apply traditional methods and automated algorithms to define cell types, quantify, and apply multiple modes of data analysis with highly interactive visualization to explore single cell data and cross-sample analysis
  • Data Warehouse Module: Centralize and harmonize data in an auditable & traceable repository, access data from anywhere, and live connect from excel and other tools
  • Operations Module: Manage and report standard assays (e.g. reagent and instrument qualification) with highly automated workflows and interactive dashboards to monitor
Design Module

Design Module

  • Design complex cytometry experiments with complete specification of reagents, conditions, keywords, samples and controls, and instrument control parameters
  • Export acquisition ready experiment files to instruments including BD, Cytek, BioRad ZE5, Attune & Novocyte
  • Centralized management of reagent listing to maintain consistent name
  • Enable lab automation and planning

Analysis Module

Analysis Module

  • Define cell types, quantify and annotate to precisely meet your use case using a combination of traditional gating, importing from external tools (FlowJo, DIVA XML, Gating ML), rule-based automation, automated enumeration of co-expression, and clustering
  • Explore co-expression patterns at the single cell level to drive hypotheses and discovery as well as conduct paired and unpaired differential analysis across samples for biomarker discovery, mechanism of action (MOA), and more
  • Share analysis dashboards and export reports
  • Translate hypotheses from analysis into database wide mining

Data Warehouse Module

Data Warehouse Module

  • Compatible with a wide range of instruments, import gating from FlowJo, GatingML, DIVA XML and review in Ryvett
  • Specify sample metadata and harmonize annotations including cell types and reagent names across operators, labs, experiments
  • Quantify biology in a number of ways including cross-well normalization
  • Powerful search engine across the entire warehouse
  • Live connect to data from a from various analytics tools including Excel, Tableau, Spotfire and Scripting (e.g. R, python) to support analysis and reporting
Operations Module

Operations Module

  • Automate all aspects of standardized and/or validated assays including gating, quantification and reporting with ability to review, edit & lock with audit trail
  • Computational gating rules that combine expert knowledge and ML/AI techniques to adopt gates to each dataset
  • Built in support for reagent and instrument qualification and monitoring
  • Centralize data with live dashboards for monitoring, standardized reporting, and supporting quality systems
  • Rapidly configure new assay formats to transition from R&D to standardized assays


Single cell application for multi-omics data

  • Automatically unmix barcoded sample data with interactive visuals to refine and QC
  • Add or upload sample annotations
  • Define cell types by traditional gating or automated methods, quantify counts, frequencies and other metrics
  • Apply standard filtering methods and normalization to RNA data
  • Conduct differential and other analyses using antibody and RNA data
  • Perform highly interactive analyses via results dashboard with visual (UMAP and more), create statistical summaries and downloadable report
  • Easy to use interface for research scientists and strong API for bioinformaticians to interface with new algorithms and methods
  • Share and Collaborate with others


For multiplex bead assays

PlexScope is a cloud-based software platform designed to provide highly automated data processing and reporting for multiplex bead data. Raw data to computed concentrations in minutes with easy to use interface accessible via browser:

  • Raw data to computed concentrations in minutes with easy to use interface, accessible via browser
  • Software integrated with your bead panels, if desired at the lot level
  • Machine learning driven bead identification, that is highly accurate (> 98%) and extensively tested
  • Highly interactive results dashboard with visual and statistical summaries
  • Secure data transfer and built-in user specific access control
  • Share and Collaborate with others
Panels of Antibodies

Panels of Antibodies

  • Predefined panels with no manual entry
  • Standardized annotations
  • Lot level integration with easy specification of replicates and dilution

Auto-Gate Beads

Auto-Gate Beads

  • Fully automated and highly accurate identification of beads
  • Easy to use review and edit functionality

Data Analysis

Data Analysis

  • Highly interactive results dashboard
  • Built in statistical basis for choice of curve
  • Downloadable report