The Most Powerful & Intuitive Single Cell Analysis Solution Available

Analyze your single cell data with intuitive point-and-click actions using Partek Flow bioinformatics software. No command-line experience is needed. It combines the powerful statistics you trust with information-rich, interactive visualizations to take your analysis from start-to-finish. It’s as simple as point, click, and done.

Three-Minute Tour of Our Single Cell Analysis Solution

Single Cell Applications Supported

  • Single Cell RNA-Seq
  • Single Nucleus RNA-Seq
  • CITE-Seq
  • ECCITE-Seq (CRISPR compatible)
  • TotalSeq
  • REAP-Seq
  • Feature Barcoding
  • Cell Hashing
  • Antibody Capture Sequencing
  • Flow Cytometry/Mass Cytometry
  • V(D)J
  • Spatial Transcriptomics
  • Single Cell ATAC-Seq with or without scRNA-Seq

Covering the Complete Single Cell Analysis Process

Import data from any major single cell platform and take your analysis from start to finish.

Single Cell Analysis Process

Interactive Visualizations in Partek Flow

Explore biological insights in your data with fully customizable visualizations and create high quality images for your publications.

CHI square table in Partek Flow

Multiomics Analysis

Easily integrate and visualize RNA-Seq and ATAC-Seq, or other assays

Partek Flow Pie Charts

Cell Type Abundance

Determine cell type abundance using a variety of plot types

Partek Flow Spatial Visualization

Spatial Transcriptomics

Overlay gene expression data to visualize spatial morphology

Partek Flow Trajectory

Trajectory Analysis

Analyze biological processes using trajectories

Partek Flow t-SNE

Classification of Cells

Classify cells by traditional methods or automatically

Partek Flow Violin Plot

Differential Analysis

Detect gene expression by type using a dot/violin plot

Partek Flow Heatmap

Hierarchical Clustering

Customize heatmaps based on gene lists

KEGG Pathway visualization in Partek Software

Biological Interpretation

Discover meaningful biological insights using integrated pathways

Frequently Asked Questions

Your analysis can start with fastq/bcl, count matrix, or Seurat objects.

Partek Flow offers many ways to interact with and present your data. Here is a quick summary of some of the available options: PCA, t-SNE, UMAP, volcano plots, heatmaps, bubble maps, Venn diagrams, dot plots, KEGG pathways, Sankey plots, histograms, TSS plots, pie charts, cell trajectory graphs, knee plots, scatter plots (2D or 3D), bar charts, tissue spot histology images, violin plots, and box-whisker plots.

There are multiple ways to classify cells in Partek Flow, including the Garnett algorithm for automatic cell classification.

Yes, you can create and import custom gene lists for analysis. Additionally, Partek Flow provides access to hosted gene lists curated from a variety of popular publications.

Yes, we offer web-based training sessions for first-time users and ongoing analysis assistance. Additionally, we provide access to online documentation and a variety of webinars and training videos.

Export data at any stage of the analysis process including the whole project, visualizations, or pipelines.

Process Data from Any Single Cell Technology

Single cell platforms supported by Partek Flow

Powerful Tools & Features in an Easy-to-Use Application:

Taxonomic classification Automatic or Manual Cell Classification
Classify your cells by traditional methods or automatic cell classification using regression-based methods for human and mouse.
visualization icon Interactive Visualization
Modify data-rich visualizations with direct manipulation to drill down to the details you need and export in publication-ready formats.
statistical algorithms Powerful Industry-Standard Statistics
The gold standard statistical methods you need to find differences, similarities, or even factors influencing survival rate.
data icon Easy Data Import and Export
Import any fastq/bcl, count matrix file, or Seurat object and export your analysis at any point in industry-standard formats.
QA/QC icon Robust QA/QC Capabilities
A variety of quality assurance/control tools and reports are available for unaligned and aligned reads allowing you to evaluate the status of your analysis and optimize downstream viability.
Differential analysis Multi-Sample Analysis
Analyze and visualize multiple samples together or independently and discover biological variations with combined and split-by-sample analysis.
Differential analysis Flexible Differential Analysis 
Powerful statistical analysis tools help you determine patterns and markers in datasets, including genes, proteins, and pathways.
pathway analysis Complete and Unbiased Biological Interpretation
Learn more about the biology underlying gene expression changes in your data using gene ontology (GO) or pathway enrichment analysis.
scale icon Discover Biomarkers that Define a Cell Population
Use biomarkers to define a cell population, condition, or another parameter within your study.
test tub icon Compare Cell Type Populations Between Experimental Groups
Whether it’s rare or common cell types, our extensive statistical models can help make meaningful comparisons.
Human single cells with chromosomes, 3D illustration Learn about the single cell analysis process, popular assays,
and access detailed training material in our Single Cell Resource Guide.
Kathi GoscheSingle Cell Gene Expression