CUT&RUN Data Analysis
Novel epigenetics discoveries in minutes. Transform raw data into interactive plots, all in your browser.

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Trusted by high-velocity scientific teams


The intuitive data & analysis platform you've been looking for


Pluto is an end-to-end discovery platform built for life science teams. Get started analyzing your CUT&RUN data in minutes, with no need to set up bioinformatics pipelines or manage infrastructure.
Tip: Pluto supports 20+ assays besides CUT&RUN. You can upload FASTQ files or tabular results to begin visualizing results right away!

Industry-best visualizations, all in one place

Science moves fast - your team deserves software that can keep up. Instead of using 5+ disparate tools to analyze your CUT&RUN data, create all of the exploratory visualizations you need in one place.  Search, embed, and share your results, then customize final, publication-ready figures for export.

Tip: In Pluto, every analysis has its own, fully dynamic methods section, including all analysis parameters and relevant references.

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Built for scientific teams that scale: No per-sample or per-user costs

Single annual platform fee, so your team knows the entire cost upfront. No uncontrolled costs, or using fewer samples to minimize expense.

Customizable, publication-quality results and figures

Easily customize colors and visual appearance for beautiful plots, every time. Apply company-approved color palettes for consistency.

We manage the pipelines so you don't have to

70% of teams time is spent managing the systems to support the analysis.  We do this for you, so you can spend 100% of your time making discoveries.

Flexible and data-driven to support different experimental designs 

  • Annotate samples with relevant metadata
  • Your annotations customize analyses
  • R&D, preclinical, or clinical sample types
  • Organize both in vivo and in vitro studies

Native analysis and visual capabilities for CUT&RUN data 

  • FASTQ file storage
  • Alignment and processing pipeline
  • Detailed QC metrics and reporting
  • Interactive, biology-focused analysis

Plus, support for 20+ more assays, all in one platform

  • Epigenetics
  • Transcriptomics
  • Low-throughput assays (e.g. qPCR, ELISA)
  • And more! 

Side by side analysis 

Store multiple CUT&RUN experiments in Pluto for comparison and organization

Collaborate and share, securely

Invite internal or external collaborators with role based permissions. 

See it in action, schedule a demo today   

Beyond CUT&RUN Pluto can manage RNA-seq, low throughput experiments, and much more. 


Analysis and plot types

Differential binding analysis

Identify targets that are differentially bound under different conditions

Calculate statistically significance using bioinformatics best-practices (no coding required)

Peak analysis and IGV plots

Visualize signal-to-background
Look at peaks of interest in different samples with integrative genome viewer (IGV)

Pathway analysis

See top changed pathways and compute pathway-level statistics

Summarize counts with bar, box and heatmap plots

Visualize intra-sample variability with normalized or raw counts

Longitudinal analysis with line plots

See how binding changes over time or with increasing dose

Dimensionality reduction analysis

See how your samples cluster over time or with increasing dose

Pluto has more analysis and plot types - talk to our science advisors about how we can make Pluto work for you

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