diff --git a/pre-release/404.html b/pre-release/404.html index 3f07b38..ecc2fc4 100644 --- a/pre-release/404.html +++ b/pre-release/404.html @@ -1 +1 @@ - FlowJo Report

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\ No newline at end of file diff --git a/pre-release/index.html b/pre-release/index.html index 60d59f7..e509a90 100644 --- a/pre-release/index.html +++ b/pre-release/index.html @@ -1 +1 @@ - FlowJo Report
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Table of Contents

Table of Contents

Introduction to the step by step guide

Create Project

Preparation of the 3 files

Uploading the data

Finding the template

Open the workflow

Gather Step

Join Step

Wizard Step

Checking if all the annotation are correct

Create Filter

Customization of Plots

Download the Data and Plots

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

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

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 annotation are correct

Checking if all 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 diff --git a/pre-release/search/search_index.json b/pre-release/search/search_index.json index 72ab83d..3507e91 100644 --- a/pre-release/search/search_index.json +++ b/pre-release/search/search_index.json @@ -1 +1 @@ -{"config":{"lang":["en"],"separator":"[\\s\\-]+","pipeline":["stopWordFilter"]},"docs":[{"location":"","title":"Home","text":""},{"location":"#table-of-contents","title":"Table of Contents","text":"

Table of Contents

Introduction to the step by step guide

Create Project

Preparation of the 3 files

Uploading the data

Finding the template

Open the workflow

Gather Step

Join Step

Wizard Step

Checking if all the annotation are correct

Create Filter

Customization of Plots

Download the Data and Plots

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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.

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

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You require three files

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.

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When uploading the data:

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I copied it from a project

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Run the join

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Checking if all there is one single value per cell

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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.

"},{"location":"#create-project","title":"Create Project","text":"

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

"},{"location":"#preparation-of-the-three-files","title":"Preparation of the three files","text":"

You require three files

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.

"},{"location":"#uploading-the-data","title":"Uploading the data","text":"

When uploading the data:

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I copied it from a project.

"},{"location":"#open-the-workflow","title":"Open the workflow","text":""},{"location":"#gather-step","title":"Gather Step","text":""},{"location":"#join-step","title":"Join Step","text":"

Run the join

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Checking if there is one single value per cell

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