Tutorials

The following are step-by-step examples to get you started using Cytoflow. They include both some basic tutorials as well as examples of some more advanced analyses.

Easy tutorials

• Tutorial: Quickstart
  • Importing data
  • Basic plotting
  • Basic gating
  • Basic statistics
  • Export the plot
• Tutorial: Dose-Response
  • Importing Data
  • Filter out clumps and debris
  • Look at the FITC_A channel
  • Summarize the dose-response curve on a line plot
  • Export the dose-response curve as a table
• Tutorial: Hierarchical Gating
  • Import the data
  • Gate single cells and live cells
  • Create Immune Cell Phenotype Gates
  • Analyze the hierarchy
• Tutorial: Estimating Genome Size
  • Import the data
  • Take a look at the data
  • Gate out the high SSC events
  • Find the peaks with a density gate
  • Separate the control and the sample peak
  • Compute the peaks’ means
• Tutorial: Microbial Diversity
  • Preprocessing
  • Import the data
  • Preview and gate the data
  • Cluster with a self-organizing map
  • Count events in each cluster

Advanced tutorials

• Tutorial: Yeast Multidimensional Induction Timecourse
  • Import the data
  • Filter out clumps and debris
  • Compute the geometric mean at each different timepoint and IP concentration
  • Is a geometric mean an appropriate summary statistic?
  • Model the data as a mixture of gaussians
• Tutorial: Synthetic Gene Logic Network
  • Import the data
  • Gate out debris
  • Select transfected cells
  • Examine the function of the gene circuit
  • Further exploration
• Tutorial: Transcriptional Repressor Characterization
  • Setup
  • Gate out the debris
  • TASBE Calibration
  • Binned Analysis
  • Creating Transfer Curves
• Tutorial: Machine Learning
  • Import the data
  • Examine the data
  • Create a Gaussian mixture model
  • Advanced GMM uses
  • More Machine Learning Operations
• Tutorial: Computational Cytometry
  • Import the data
  • Gate for single, live cells
  • Clustering with self-organizing maps
  • t-distributed Stochastic Neighbor Embedding