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Introduction to the step-by-step guide

Here are step-by-step instructions on how to run the FlowJo stat workflow.
This workflow allows the automation and parallelization of many plot analyses.

Create Project

Create a Project in Tercen
Note: If you create in a Team, then you can share it easier

Preparation of the three files

You require three files

  • Measurement file
  • Sample annotation file
  • Display name file

These can be created from the Flowjo Export Table file

Here is a link to a template of the three files.
Download them and fill them out.

Uploading the data

When uploading the data:

  • ATP import as “character”
  • SEB import as “character”
  • Days import as “character”

Finding the template

I copied it from a project.

Open the workflow

Gather Step

  • Remove all and add all

Join Step

Run the join

Wizard Step

Question Action Remark
"Select the samples column from the measurement file (i.e., FlowJo file). Examples: `samples samples Had to select
"Select the samples column from the sample annotation file. Examples: `sample.samples` sample.samples Automatically selected
"Select the ELN column from the sample annotation file, otherwise, leave blank. Examples: `sample.ELN`", sample.ELN Had to select
No selection necessary, click Next exp.variable Automatically selected
No selection necessary, click Next cellpop.Flowjo name Automatically selected
No selection necessary, click Next cellpop.Display name Automatically selected
No selection necessary, click Next Cell.pop Display name “NA” “ “ Automatically selected
No selection necessary, click Next cell.pop.Display name “NA” “ “ Automatically selected
No selection necessary, click Next exp.value Automatically selected
"Select the factors representing the conditions. Multiple selections are possible. Examples: `sample.compound`, `sample.ATP`, `sample.Ab`, `sample.Ab2` and etc..", sample.Ab sample.Ab2 sample.treatment sample.STP sample.SEB Manually selected
Selecting the control per condition (z-score on mean) Filters - Select your control compound/condition sample.treatment = DMSO ATP =0 SEB =1 Ab= PD1 Ab2 = Belrestotug Manually selected Apply filter

Checking if all the annotations are correct

Checking if there is one single value per cell

Create Filter

Customization of Plots

Point plot 2Gb
Barplot (mean) with jitter 2Gb
Barplot (mean) with sd error bars 2Gb
Heatmap 2Gb, 1000x3000

Download the Data and Plots

\ No newline at end of file + FlowJo Report
Skip to content

Introduction to the step-by-step guide

Here are step-by-step instructions on how to run the FlowJo stat workflow.
This workflow allows the automation and parallelization of many plot analyses.

Create Project

Create a Project in Tercen
Note: If you create in a Team, then you can share it easier

Preparation of the three files

You require three files

  • Measurement file
  • Sample annotation file
  • Display name file

These can be created from the Flowjo Export Table file

Here is a link to a template of the three files.
Download them and fill them out.

Uploading the data

When uploading the data:

  • ATP import as “character”
  • SEB import as “character”
  • Days import as “character”

Finding the template

I copied it from a project.

Open the workflow

Gather Step

  • Remove all and add all

Join Step

Run the join

Wizard Step

Question Action Remark
"Select the samples column from the measurement file (i.e., FlowJo file). Examples: `samples samples Had to select
"Select the samples column from the sample annotation file. Examples: `sample.samples` sample.samples Automatically selected
"Select the ELN column from the sample annotation file, otherwise, leave blank. Examples: `sample.ELN`", sample.ELN Had to select
No selection necessary, click Next exp.variable Automatically selected
No selection necessary, click Next cellpop.Flowjo name Automatically selected
No selection necessary, click Next cellpop.Display name Automatically selected
No selection necessary, click Next Cell.pop Display name “NA” “ “ Automatically selected
No selection necessary, click Next cell.pop.Display name “NA” “ “ Automatically selected
No selection necessary, click Next exp.value Automatically selected
"Select the factors representing the conditions. Multiple selections are possible. Examples: `sample.compound`, `sample.ATP`, `sample.Ab`, `sample.Ab2` and etc..", sample.Ab sample.Ab2 sample.treatment sample.STP sample.SEB Manually selected
Selecting the control per condition (z-score on mean) Filters - Select your control compound/condition sample.treatment = DMSO ATP =0 SEB =1 Ab= PD1 Ab2 = Belrestotug Manually selected Apply filter

Checking if all the annotations are correct

Checking if there is one single value per cell

Create Filter

Customization of Plots

Point plot 2Gb
Barplot (mean) with jitter 2Gb
Barplot (mean) with sd error bars 2Gb
Heatmap 2Gb, 1000x3000

Download the Data and Plots

\ No newline at end of file