Tutorial transcript #443

anikde07 · 2025-01-27T13:17:44Z

Draft Pull request for a first version of the transcript.
To do:

Clean the last paragraph
Screenshot and markup website

Initial text

LeaSeep

I feel like there are still a lot of grammar, language issues - please revise

LeaSeep · 2025-01-30T16:22:57Z

docs/Transcript.md

+title: "Transcript of Tutorial"
+output: html_notebook
+---
+Welcome to cOmicsArt - Customizable Omic Analysis and Reporting Tool. This tutorial is going to show you how to use this application to aid in your statistical analysis.


Suggested change

Welcome to cOmicsArt - Customizable Omic Analysis and Reporting Tool. This tutorial is going to show you how to use this application to aid in your statistical analysis.

Welcome to cOmicsArt - Customizable Omic Analysis and Reporting Tool. This tutorial is going to show you how to use this application to guide your statistical analysis.

LeaSeep · 2025-01-30T16:23:23Z

docs/Transcript.md

+Welcome to cOmicsArt - Customizable Omic Analysis and Reporting Tool. This tutorial is going to show you how to use this application to aid in your statistical analysis.
+This tutorial is self-contained but can also be used to follow along with the YouTube tutorial.
+
+Comics art is designed is in a tabular format. In the beginning you only see the data selection but if you upload your data and go through the steps progressively more 


Suggested change

Comics art is designed is in a tabular format. In the beginning you only see the data selection but if you upload your data and go through the steps progressively more

cOmicsArt is designed is in a tabular format. In the beginning you only see the 'data selection'-tab but if you upload your data and go through the steps progressively more

LeaSeep · 2025-01-30T16:27:06Z

docs/Transcript.md

+
+## Uploading Data ##
+
+The data will be uploaded with three CSV files. The first one is the data matrix showing the counts on the rows there are the entities for example genes on the columns 


Suggested change

The data will be uploaded with three CSV files. The first one is the data matrix showing the counts on the rows there are the entities for example genes on the columns

The data can be uploaded using three CSV files.

The first file is the data matrix showing the counts on the rows there are the entities for example genes on the columns

This is not proper english

LeaSeep · 2025-01-30T16:27:34Z

docs/Transcript.md

+## Uploading Data ##
+
+The data will be uploaded with three CSV files. The first one is the data matrix showing the counts on the rows there are the entities for example genes on the columns 
+they are the samples. The sample table shows you meta information on the samples while the entity table shows you any information on the entities you have. 


both is metadata

LeaSeep · 2025-02-16T14:08:14Z

I have pushed a commit with adjustments of the text to guide you what I was expecting. Please revise the entire transcript, by reading through it and adjust for actual readability it still contains too many language errors.
Deviations from what is actually said in the tutorial are totally acceptable - sentences should be more concise mostly

anikde07 · 2025-02-27T22:41:50Z

I have revised the transcript for all sections except Pre-Processing and Sample Correlation.
Let me know if the revised sections now look better and what further changes need to be made to them.
According to these I will revise the Pre-Processing and Sample Correlation sections.

LeaSeep

Please address all comments and suggestions.
Additioanlly add at the top a disclaimer that the tutorial was based on cOmicsArt v.1.0.0 and that some parts of the interface e.g. where to find options has changed and additional options also added but that the majority also within this tutorial can be readily still used

LeaSeep · 2025-03-04T10:18:49Z

docs/Transcript.md

+
+To upload your data, you'll need three CSV files:  
+
+- **The data matrix**, where rows represent entities (like genes) and columns represent samples. The values contain count data.  


Suggested change

- **The data matrix**, where rows represent entities (like genes) and columns represent samples. The values contain count data.

- **The data matrix**, where rows represent entities (like genes) and columns represent samples. The values contain e.g. count data.

LeaSeep · 2025-03-04T10:19:55Z

docs/Transcript.md

+
+[Caption of screenshot] This documentation shows you how to upload your data via the file input. 
+
+We choose an example data set which is also available for download:  


Suggested change

We choose an example data set which is also available for download:

We choose the example data set which is also available for download:

LeaSeep · 2025-03-04T10:21:00Z

docs/Transcript.md

+At the bottom of the screen there are a multitude of checks where you can check whether your data looks as it should be.
+Green signifies that the dataset is fine, whereas red means you need to go into your data and change things and orange means the dataset has some issues but the program can handle it - for example this dataset contains some entries which are missing and the application will just remove those entities from the table.
+
+After the inspection of the data is complete, click on "Upload new data" and now you should see your result in the right hand section of the panel.


Suggested change

After the inspection of the data is complete, click on "Upload new data" and now you should see your result in the right hand section of the panel.

After the inspection of the data is completed, click on "Upload new data" and now you should see your result in the right hand section of the panel.

LeaSeep · 2025-03-04T10:21:53Z

docs/Transcript.md

+
+For the sample selection we first choose among the columns present in the sample table. For example we can choose the cells, condition, experiment or the sample. 
+If we select sample, additionally we can select only specific samples we want to include the data analysis. Perhaps there are strong reasons to exclude some samples. By clicking on the specific sample, it removes all other samples and only uses the selection of samples we made.
+If we select condition, we can do a similar selection. Here it's treated or untreated but you have multiple conditions you might want to only check one of them. 


Suggested change

If we select condition, we can do a similar selection. Here it's treated or untreated but you have multiple conditions you might want to only check one of them.

If we select condition, we can do a similar selection. Here, it's treated or untreated but you have multiple conditions you might want to only check one of them.

LeaSeep · 2025-03-04T11:49:50Z

docs/Transcript.md

+Here you can see the design choice for the layout, which remains consistent for the other the data analysis windows we will cover: 
+The left side consists of the sidebar with all the available options. Additionally, the options which need re-computation on being changed are separated from those which do not such re-computation by a separating line.
+
+For example we can choose the vst_DESeq, and then choose the genes. [?]


Does not make sense

Do you mean in the last line mentioning vst_DESeq? If this is the part then, I could not understand what Paul meant by choosing vst_DESeq and then choosing the genes.

LeaSeep · 2025-03-04T12:45:39Z

docs/Transcript.md

+
+Example:
+We select the following three comparisons: "N052611:N61311", "N080611:N61311", "N061011:N61311". 
+For this comparison, when we look at adjusted p-values, the result visualization is currently empty because we have nothing significant. 


try to stick to one notation for writing 'p-values'
ABove there is also 'P values', 'p values' etc

LeaSeep · 2025-03-04T12:45:51Z

docs/Transcript.md

+We select the following three comparisons: "N052611:N61311", "N080611:N61311", "N061011:N61311". 
+For this comparison, when we look at adjusted p-values, the result visualization is currently empty because we have nothing significant. 
+
+But if we choose to look at raw P values by changing the type of significance to "significant unadusted", there is now a plot which shows the genes which are significant in each of the comparisons.


Suggested change

But if we choose to look at raw P values by changing the type of significance to "significant unadusted", there is now a plot which shows the genes which are significant in each of the comparisons.

But if we choose to look at raw P values by changing the type of significance to "significant unadjusted", there is now a plot which shows the genes which are significant in each of the comparisons.

LeaSeep · 2025-03-04T12:46:45Z

docs/Transcript.md

+First, we select between raw or pre-processed data and then select the gene to visualise from the list of available genes under "Select the Gene from the list".
+On selecting the "Get Single Gene Visualisation", we get box plots or dot plots. Box plots will only be visible if you have more than 3 samples per group. If there are fewer than 4 samples, only dots will be displayed. 
+
+You can also group the samples based on the annotation categories by choosing the annotation category from the list of available categories under "Choose the groups to show the data for"


Suggested change

You can also group the samples based on the annotation categories by choosing the annotation category from the list of available categories under "Choose the groups to show the data for"

You can also group the samples based on the annotation categories by choosing the annotation category from the list of available categories under "Choose the groups to show the data for".

LeaSeep · 2025-03-04T12:48:01Z

docs/Transcript.md

+
+For each gene set selected a tab will be visible within which you can see the enrichment. 
+
+[Again for the tables you can download the tables and for the plots you have sent only through report get the underlying R code to reproduce this in R directly or save the plot as it is the]


What is this bracket notation for?

The bracket notation is for the lines which are repeated a couple of times for example Paul goes through how to save and report the plots a couple of times across the various tabs and I was not sure if we should keep this reporting section in the transcript every-time it is mentioned in the tutorial

LeaSeep · 2025-03-04T12:48:24Z

docs/Transcript.md

+
+We now come to the Heatmap tab. 
+
+The Heatmap displays the count matrix in a clustered fashion and We now can select what entities we want to plot. 


Suggested change

The Heatmap displays the count matrix in a clustered fashion and We now can select what entities we want to plot.

The Heatmap displays the count matrix in a clustered fashion and we now can select what entities we want to plot.

anikde07 added 2 commits January 25, 2025 20:52

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LeaSeep marked this pull request as ready for review February 16, 2025 13:42

read through till pre-processing

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Revised all sections except Pre-Processing and Sample Correlation

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Tutorial transcript #443

Tutorial transcript #443

anikde07 commented Jan 27, 2025

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anikde07 Mar 4, 2025 •

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	Welcome to cOmicsArt - Customizable Omic Analysis and Reporting Tool. This tutorial is going to show you how to use this application to aid in your statistical analysis.
	Welcome to cOmicsArt - Customizable Omic Analysis and Reporting Tool. This tutorial is going to show you how to use this application to guide your statistical analysis.

	Comics art is designed is in a tabular format. In the beginning you only see the data selection but if you upload your data and go through the steps progressively more
	cOmicsArt is designed is in a tabular format. In the beginning you only see the 'data selection'-tab but if you upload your data and go through the steps progressively more


		## Uploading Data ##

		The data will be uploaded with three CSV files. The first one is the data matrix showing the counts on the rows there are the entities for example genes on the columns

	The data will be uploaded with three CSV files. The first one is the data matrix showing the counts on the rows there are the entities for example genes on the columns
	The data can be uploaded using three CSV files.
	The first file is the data matrix showing the counts on the rows there are the entities for example genes on the columns


		To upload your data, you'll need three CSV files:

		- The data matrix, where rows represent entities (like genes) and columns represent samples. The values contain count data.


		[Caption of screenshot] This documentation shows you how to upload your data via the file input.

		We choose an example data set which is also available for download:

	We choose an example data set which is also available for download:
	We choose the example data set which is also available for download:

	After the inspection of the data is complete, click on "Upload new data" and now you should see your result in the right hand section of the panel.
	After the inspection of the data is completed, click on "Upload new data" and now you should see your result in the right hand section of the panel.

	If we select condition, we can do a similar selection. Here it's treated or untreated but you have multiple conditions you might want to only check one of them.
	If we select condition, we can do a similar selection. Here, it's treated or untreated but you have multiple conditions you might want to only check one of them.

	But if we choose to look at raw P values by changing the type of significance to "significant unadusted", there is now a plot which shows the genes which are significant in each of the comparisons.
	But if we choose to look at raw P values by changing the type of significance to "significant unadjusted", there is now a plot which shows the genes which are significant in each of the comparisons.

	You can also group the samples based on the annotation categories by choosing the annotation category from the list of available categories under "Choose the groups to show the data for"
	You can also group the samples based on the annotation categories by choosing the annotation category from the list of available categories under "Choose the groups to show the data for".


		For each gene set selected a tab will be visible within which you can see the enrichment.

		[Again for the tables you can download the tables and for the plots you have sent only through report get the underlying R code to reproduce this in R directly or save the plot as it is the]


		We now come to the Heatmap tab.

		The Heatmap displays the count matrix in a clustered fashion and We now can select what entities we want to plot.

Tutorial transcript #443

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Tutorial transcript #443

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LeaSeep commented Feb 16, 2025

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anikde07 Mar 4, 2025 •

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