Pluto Bio Platform

Pluto Bio is a multi-omics platform designed for translational discovery in life sciences, enabling computational biology analyses, biological data organization, and powerful visualizations — all without requiring programming expertise. Built for mission-focused life sciences organizations, Pluto empowers biologists, bioinformaticians, science leads, and managers to run gold-standard analyses, explore multi-omics datasets, and collaborate in real time through an intuitive canvas interface.

The platform consolidates the full analytical workflow — from raw data import to publication-ready figures — into a single unified environment, eliminating bottlenecks and enabling every team member to contribute to scientific discovery regardless of their coding background.

Supported Assays and Analyses

• Single Cell RNA-seq: Dissect cellular heterogeneity using flexible preprocessing workflows, analyze individual cell gene expression profiles, and uncover cellular diversity and function by cell type and condition.
• Spatial Transcriptomics: Analyze gene expression while retaining spatial context, and visualize transcript distribution across tissue sections to understand spatial organization of cells and biological processes.
• Bulk RNA-seq: Analyze gene expression at a genome-wide scale to uncover differential expression, altered regulatory pathways, transcriptional networks, and individual biomarkers and targets.
• CUT&RUN and CUT&Tag: Profile chromatin and transcription factor binding sites to enhance epigenetic insights using efficient, streamlined methods.
• ChIP-seq: Map global binding sites for histones, transcription factors, or any protein of interest and visualize results directly in the platform.
• ATAC-seq: Characterize the chromatin landscape and gain insights into regulatory regions and gene expression control through simplified chromatin accessibility analysis.
• PRO-seq: Map transcriptional activity with precision by revealing RNA Polymerase II binding sites for a detailed view of gene regulation.
• Proteomics: Analyze unbiased or targeted proteomics datasets, create signatures, identify biomarkers, and explore inter- and intra-sample variability.
• Multi-omics: Integrate diverse assay data — including bulk RNA-seq, ATAC-seq, ChIP-seq, and more — into a unified multi-omics experiment for in-depth insights into cellular processes and disease mechanisms.
• Custom Pipelines: Design and execute complex bioinformatics workflows tailored to unique research requirements.

Analytical Capabilities

• Differential Analyses: Investigate genome-wide gene expression, binding, protein levels, and more using gold-standard computational biology algorithms, with flexible comparison of conditions, treatments, and study variables.
• Dimensionality Reduction: Utilize PCA, UMAP, and t-SNE to uncover patterns and relationships in high-dimensional data and facilitate intuitive sample clustering.
• Functional Analysis: Uncover biological functions and pathways using GO and KEGG tools for a comprehensive view of the biological context underlying results.
• Pathway Analyses: Explore molecular pathways driving biological functions and diseases using GSEA, TFEA, ORA, and STRING to discover critical interactions and regulatory networks.
• Over-Representation Analysis (ORA): Identify enriched pathways and biological processes by comparing data against known gene sets.
• Marker Expression: Investigate expression of specific marker genes across single-cell RNA-seq data using customizable ridge plots, violin plots, and UMAP projections.
• Longitudinal Analysis: Track changes over time to examine temporal and continuous data, study developmental stages, treatment responses, and disease progression.
• Imaging: Annotate and quantify images directly within the platform, integrating morphological data with molecular analyses.
• Summary Analysis: Quickly summarize and compare raw or normalized data across user-defined groups for concise overviews of experimental results.

Data Visualization

• Biology-specific visualizations are available to every team member with no programming required.
• Supported plot types include: bar plots, boxplots, scatterplots, volcano plots, heatmaps, Kaplan-Meier curves, line plots, enrichment plots, top pathways plots, Integrative Genome Viewer (IGV) plots, tornado plots, TSS profile plots, cluster plots, ridge plots, violin plots, UMAP plots, images, and GraphPad Prism figures.
• Users can explore thousands of single-cell data points, inspect genomic regions across different organisms, and customize appearance to ensure accuracy and on-brand presentation.

Data Security and Compliance

• SOC2 Type II: Pluto maintains an AICPA SOC 2 Type 2 report with continuous monitoring of adherence to SOC 2 controls, with real-time compliance status available via the Trust Center.
• End-to-End Encryption: Data is encrypted both in transit (TLS) and at rest (AES256), with security built into all data transfer mechanisms.
• GDPR Compliance: Pluto is fully GDPR compliant with robust data protection controls, continuous monitoring, and a dedicated GDPR EU representative.
• Role-Based Access Controls: Stringent individual privacy protections are enforced through role-based permissions and access controls.
• Trust Center: Real-time monitoring covers infrastructure security, organizational security, product security, internal security procedures, and data and privacy.

Infrastructure and Collaboration

• Cloud-Scaled Compute: Handles datasets of any size without computational bottlenecks; all storage and compute are included in Pluto subscriptions with no hidden or usage-based costs.
• Advanced Data Integration: Integrates diverse data types — genomic sequences, proteomic profiles, clinical data — into a unified platform for comprehensive analysis.
• Real-Time Collaboration: Supports synchronous editing, comments, and discussion threads, enabling teams to share findings, datasets, and analyses instantly with colleagues worldwide.
• Pluto API: Provides developers with programmatic access to platform entities for custom workflow automation.
• Export Options: Plots, methods, references, and other information can be exported to Microsoft Word and Microsoft PowerPoint.

Integrations

• BaseSpace: Import FASTQ files directly from Illumina's cloud platform to run RNA-seq, ChIP-seq, CUT&RUN, and other pipelines.
• Azure Active Directory and SAML 2.0: Enterprise-grade single sign-on compatible with any identity management platform (IDP).
• Okta and Google Sign-in: Additional single sign-on options for seamless user authentication.
• Benchling: Close the loop from initial experiment planning to final analysis within a unified research and development workflow.
• Notion, Coda, Colabra, and Smartsheet: Embed live, interactive Pluto plots directly into documents, notebooks, and dashboards to keep teams in sync.
• Airtable: Automatically integrate Pluto results into collaborative low-code workflows.
• Genewiz by Azenta and Novogene: Import FASTQ files directly from sequencing providers to go straight from sequencing to analysis.
• Gene Expression Omnibus (GEO): Investigate public functional genomics data without needing to wrangle file formats or write custom scripts.
• Synapse | Sage Bionetworks: Import governed datasets from Synapse directly into Pluto for analysis.
• HGNC and OMIM: Gene names and disease annotations are automatically linked and annotated upon data upload, accelerating biological investigation.

Pluto Bio is a cloud-based platform suitable for life sciences organizations of all sizes, offering comprehensive compliance certifications (SOC2 Type II, GDPR), seamless integrations with the tools research teams already use, and a collaborative ecosystem designed to accelerate translational discovery from data to insight.