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-# Home
+## Table of Contents {#table-of-contents}
+
+[Table of Contents](#table-of-contents)
+
+[Introduction to the step by step guide](#introduction-to-the-step-by-step-guide)
+
+[Create Project](#create-project)
+
+[Preparation of the 3 files](#preparation-of-the-3-files)
+
+[Uploading the data](#uploading-the-data)
+
+[Finding the template](#finding-the-template)
+
+[Open the workflow](#open-the-workflow)
+
+[Gather Step](#gather-step)
+
+[Join Step](#join-step)
+
+[Wizard Step](#wizard-step)
+
+[Checking if all the annotation are correct](#checking-if-all-the-annotation-are-correct)
+
+[Create Filter](#create-filter)
+
+[Customization of Plots](#customization-of-plots)
+
+[Download the Data and Plots](#download-the-data-and-plots)
+
+## Introduction to the step by step guide {#introduction-to-the-step-by-step-guide}
+
+Here is a step by step instruction on how to run the FlowJo stat workflow.  
+It is a workflow allowing automation and parallelization of many plots analysis.
+
+## Create Project {#create-project}
+
+Create a Project in Tercen  
+Note: If you create in a Team then you can share it easier
+
+## Preparation of the 3 files {#preparation-of-the-3-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.
+
+## Uploading the data {#uploading-the-data}
+
+When uploading the data:
+
+* ATP import as “character”  
+* SEB import as “character”  
+* Days import as “character”
+
+## Finding the template {#finding-the-template}
+
+I copied it from a project
+
+## Open the workflow {#open-the-workflow}
+
+### Gather Step {#gather-step}
+
+* Remove all and add all
+
+### Join Step {#join-step}
+
+Run the join
+
+### Wizard Step {#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 annotation are correct {#checking-if-all-the-annotation-are-correct}
+
+Checking if all there is one single value per cell
+
+### Create Filter  {#create-filter}
+
+## Customization of Plots {#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 {#download-the-data-and-plots}