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Cytoflow 1.3.1 documentation

  • User manual
  • Developer Manual
  • GitHub
  • User manual
  • Developer Manual
  • GitHub

Section Navigation

  • Tutorials
    • Tutorial: Quickstart
    • Tutorial: Dose-Response
    • Tutorial: Hierarchical Gating
    • Tutorial: Estimating Genome Size
    • Tutorial: Microbial Diversity
    • Tutorial: Yeast Multidimensional Induction Timecourse
    • Tutorial: Synthetic Gene Logic Network
    • Tutorial: Transcriptional Repressor Characterization
    • Tutorial: Machine Learning
    • Tutorial: Computational Cytometry
  • How-To Guides
    • HOWTO: Install Cytoflow
    • HOWTO: Import an experiment from a table
    • HOWTO: Compensate for bleedthrough
    • HOWTO: Use beads to correct for day-to-day variation
    • HOWTO: Use the TASBE workflow for calibrated flow cytometry
    • HOWTO: Export FCS files
    • HOWTO: Export plots
    • HOWTO: Use different gates for different subsets of data
    • HOWTO: Add error bars to a statistics plot
  • Users’ guides
    • Guide: Using facets to compare data sets
    • Guide: Using statistics to summarize data
    • Guide: Which measure of center should I use?
    • Guide: How can I understand the experiment structure?
  • Operation and View Gallery
    • Autofluorescence correction
    • Bead Calibration
    • Binning
    • Linear Bleedthrough Compensation
    • Categorical Gating
    • Channel statistic
    • Color Translation
    • Density Gate
    • FlowClean
    • FlowPeaks Clustering
    • Gaussian Mixture Model (1D)
    • Gaussian Mixture Model (2D)
    • Hierarchical Gating
    • Import Files
    • KMeans
    • Minimum Spanning Tree Gate
    • Multi-channel statistic
    • Principal Component Analysis
    • Polygon Gate
    • Quadrant Gate
    • Range Gate
    • 2D Range Gate
    • Ratio
    • Registration
    • Self-Organizing Map Clustering
    • TASBE Calibrated Flow Cytometry
    • Threshold Gate
    • t-Stochastic Neighbor Embedding
    • Transform statistic
    • Bar Chart
    • Density Plot
    • Export FCS
    • Histogram
    • 2D Histogram
    • 1D Kernel Density Estimate
    • 2D Kernel Density Estimate
    • Long Table
    • Matrix Chart
    • Minimum spanning tree plot
    • Parallel Coordinates Plot
    • Radviz Plot
    • Scatterplot
    • 1D Statistics Plot
    • 2D Statistics Plot
    • Table
    • Violin Plot
  • Screenshots of the Cytoflow GUI
  • Frequently Asked Questions
  • User manual
  • How-To Guides

How-To Guides#

These guides are “recipes” – step-by-step guides to accomplish a particular task. They are a little higher-level than the tutorials. If there is something that you find confusing, please feel free to submit a bug report (or even better, a patch or pull request.)

  • HOWTO: Install Cytoflow
    • Windows
    • MacOS
    • Linux
  • HOWTO: Import an experiment from a table
  • HOWTO: Compensate for bleedthrough
    • Procedure
  • HOWTO: Use beads to correct for day-to-day variation
    • Procedure
  • HOWTO: Use the TASBE workflow for calibrated flow cytometry
    • Procedure
  • HOWTO: Export FCS files
    • Procedure
  • HOWTO: Export plots
    • Procedure
  • HOWTO: Use different gates for different subsets of data
  • HOWTO: Add error bars to a statistics plot

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HOWTO: Install Cytoflow

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