diff --git a/program/shinyApp/helpfiles/DataSelection_DataUploadFileInput.md b/program/shinyApp/helpfiles/DataSelection_DataUploadFileInput.md index e05652e1..4425c29f 100644 --- a/program/shinyApp/helpfiles/DataSelection_DataUploadFileInput.md +++ b/program/shinyApp/helpfiles/DataSelection_DataUploadFileInput.md @@ -1,10 +1,14 @@ ### Data Upload via File Input *** -💡 **Tip**: For more detailed information, please visit here. +
+💡 Tip: For more detailed information, please visit +this page. +
+
With `Data upload` you can upload your data to the server via explicit csv files.
-The files must be in the following format:
+The files must be in the following format:
1. data-matrix (.csv)
- contains the actual data, e.g. counts
- must have the samples (e.g. mouse 1) in the columns and a **unique** naming as @@ -22,7 +26,7 @@ The files must be in the following format:
Need help to prepare your data? Check out our Excel Workbook: UploadeHelpcOmicsArt.xlsx. -Some pitfalls you may fall into: +Some pitfalls you may fall into: * The files must be uploaded at their respective position (**data matrix, sample annotation, entities annotation**). * The files need to be **.csv** files, which also means that they need to be comma diff --git a/program/shinyApp/helpfiles/DataSelection_MetaData.md b/program/shinyApp/helpfiles/DataSelection_MetaData.md index 9ff2171f..f648db05 100644 --- a/program/shinyApp/helpfiles/DataSelection_MetaData.md +++ b/program/shinyApp/helpfiles/DataSelection_MetaData.md @@ -1,7 +1,11 @@ ### Data Upload via File Input + Meta Data Sheet *** -💡 **Tip**: For more detailed information, please visit here. +
+💡 Tip: For more detailed information, please visit +this page. +
+
With `Data upload` you can upload your data to the server via explicit csv files.
The files must be in the following format:
diff --git a/program/shinyApp/helpfiles/DataSelection_RowSelection.md b/program/shinyApp/helpfiles/DataSelection_RowSelection.md index 270df44e..82d3ed36 100644 --- a/program/shinyApp/helpfiles/DataSelection_RowSelection.md +++ b/program/shinyApp/helpfiles/DataSelection_RowSelection.md @@ -1,7 +1,11 @@ ### Data Selection by Columns and Rows *** -💡 **Tip**: For more detailed information, please visit here. +
+💡 Tip: For more detailed information, please visit +this page. +
+
With `Row selection` you can choose the entities (e.g. genes) you want to include in the analysis. diff --git a/program/shinyApp/helpfiles/DataSelection_SummarizedExp.md b/program/shinyApp/helpfiles/DataSelection_SummarizedExp.md index a39d68e1..69a721e4 100644 --- a/program/shinyApp/helpfiles/DataSelection_SummarizedExp.md +++ b/program/shinyApp/helpfiles/DataSelection_SummarizedExp.md @@ -1,7 +1,11 @@ ### Data Upload via Precompiled Data *** -💡 **Tip**: For more detailed information, please visit here. +
+💡 Tip: For more detailed information, please visit +this page. +
+
With this option, you can upload previously used data. This allows you to upload everything at once. Additionally, you can upload results from previous analyses. It is diff --git a/program/shinyApp/helpfiles/DataSelection_UploadInspection.md b/program/shinyApp/helpfiles/DataSelection_UploadInspection.md index 5dbf4416..8cf61dfa 100644 --- a/program/shinyApp/helpfiles/DataSelection_UploadInspection.md +++ b/program/shinyApp/helpfiles/DataSelection_UploadInspection.md @@ -1,7 +1,11 @@ ### Data Quality Check - Visual Inspection *** -💡 **Tip**: For more detailed information, please visit here. +
+💡 Tip: For more detailed information, please visit +this page. +
+
Using the `Upload visual inspection` tab, you can see the uploaded data and perform a data quality check. diff --git a/program/shinyApp/helpfiles/EA_Options.md b/program/shinyApp/helpfiles/EA_Options.md index 86e7be2a..88733f24 100644 --- a/program/shinyApp/helpfiles/EA_Options.md +++ b/program/shinyApp/helpfiles/EA_Options.md @@ -1,7 +1,11 @@ ## Enrichment Analysis Options *** -💡 **Tip**: For more detailed information, please visit here. +
+💡 Tip: For more detailed information, please visit +this page. +
+
In cOmicsArt you can do either a gene set enrichment analysis or an over-representation analysis. The options for both analyses are described below. For more details read here on diff --git a/program/shinyApp/helpfiles/Heatmap_Aesthetics.md b/program/shinyApp/helpfiles/Heatmap_Aesthetics.md index c4b143f4..060e2f71 100644 --- a/program/shinyApp/helpfiles/Heatmap_Aesthetics.md +++ b/program/shinyApp/helpfiles/Heatmap_Aesthetics.md @@ -1,7 +1,11 @@ ## Heatmap Aesthetics Options --- -💡 **Tip**: For more detailed information, please visit here. +
+💡 Tip: For more detailed information, please visit +this page. +
+
**1. Choose Variable to Color the Samples After:** diff --git a/program/shinyApp/helpfiles/Heatmap_FurtherOptions.md b/program/shinyApp/helpfiles/Heatmap_FurtherOptions.md index d689fe4c..4de873af 100644 --- a/program/shinyApp/helpfiles/Heatmap_FurtherOptions.md +++ b/program/shinyApp/helpfiles/Heatmap_FurtherOptions.md @@ -1,7 +1,12 @@ ## Log Fold Change (LFC) Ordering Options *** -💡 **Tip**: For more detailed information, please visit here. +
+💡 Tip: For more detailed information, please visit +this page. +
+
+ **1. Choose Type for LFC-Based Ordering:** diff --git a/program/shinyApp/helpfiles/Heatmap_Options.md b/program/shinyApp/helpfiles/Heatmap_Options.md index 85aab78e..0178dddb 100644 --- a/program/shinyApp/helpfiles/Heatmap_Options.md +++ b/program/shinyApp/helpfiles/Heatmap_Options.md @@ -1,7 +1,11 @@ ## Row Selection Options *** -💡 **Tip**: For more detailed information, please visit here. +
+💡 Tip: For more detailed information, please visit +this page. +
+
1. **Batch Correction**: Use batch-corrected data if available (set in Pre-processing). diff --git a/program/shinyApp/helpfiles/Heatmap_RowAnnoBased.md b/program/shinyApp/helpfiles/Heatmap_RowAnnoBased.md index 6afb0af6..ab9b1592 100644 --- a/program/shinyApp/helpfiles/Heatmap_RowAnnoBased.md +++ b/program/shinyApp/helpfiles/Heatmap_RowAnnoBased.md @@ -1,7 +1,11 @@ ## Additional Row Selection Options --- -💡 **Tip**: For more detailed information, please visit here. +
+💡 Tip: For more detailed information, please visit +this page. +
+
These options only make sense if you selected `rowAnno_based` in the `Row Selection`. They serve to filter the row entities which to include in the heatmap. diff --git a/program/shinyApp/helpfiles/PCA_Choices.md b/program/shinyApp/helpfiles/PCA_Choices.md index 955f989a..6201bc1d 100644 --- a/program/shinyApp/helpfiles/PCA_Choices.md +++ b/program/shinyApp/helpfiles/PCA_Choices.md @@ -1,7 +1,11 @@ ## Principal Component Analysis (PCA) Options *** -💡 **Tip**: For more detailed information, please visit here. +
+💡 Tip: For more detailed information, please visit +this page. +
+
A principal component analysis (PCA) is a linear dimensionality reduction technique to visualize clusters within your data. For a small introduction on PCAs, please refer to diff --git a/program/shinyApp/helpfiles/PreProcessing_Batch.md b/program/shinyApp/helpfiles/PreProcessing_Batch.md index 4bf0293e..53c7e630 100644 --- a/program/shinyApp/helpfiles/PreProcessing_Batch.md +++ b/program/shinyApp/helpfiles/PreProcessing_Batch.md @@ -1,6 +1,10 @@ ## Batch Correction *** -💡 **Tip**: For detailed information, visit this link. +
+💡 Tip: For more detailed information, please visit +this page. +
+
### Key Considerations: Batch correction can be performed during pre-processing if the batch information is already included in your sample annotation. When using DESeq processing, the batch-corrected data will be utilized for visualization purposes. However, for significance analysis, the batch will be treated as a factor. diff --git a/program/shinyApp/helpfiles/PreProcessing_DESeq.md b/program/shinyApp/helpfiles/PreProcessing_DESeq.md index 41cbdf6a..34d67ebd 100644 --- a/program/shinyApp/helpfiles/PreProcessing_DESeq.md +++ b/program/shinyApp/helpfiles/PreProcessing_DESeq.md @@ -1,7 +1,11 @@ ## DESeq Factor Choices *** -💡 **Tip**: For more detailed information, please visit here. +
+💡 Tip: For more detailed information, please visit +this page. +
+
### Understanding the Design Matrix in DESeq2 diff --git a/program/shinyApp/helpfiles/PreProcessing_Procedures.md b/program/shinyApp/helpfiles/PreProcessing_Procedures.md index 29b7cb16..f7da38d4 100644 --- a/program/shinyApp/helpfiles/PreProcessing_Procedures.md +++ b/program/shinyApp/helpfiles/PreProcessing_Procedures.md @@ -1,6 +1,10 @@ ## Data Preprocessing *** -💡 **Tip**: For detailed information, visit this link. +
+💡 Tip: For more detailed information, please visit +this page. +
+
### Key Steps: 1. **Cleaning:** diff --git a/program/shinyApp/helpfiles/SampleCorr_Choices.md b/program/shinyApp/helpfiles/SampleCorr_Choices.md index e3694b92..1e298b17 100644 --- a/program/shinyApp/helpfiles/SampleCorr_Choices.md +++ b/program/shinyApp/helpfiles/SampleCorr_Choices.md @@ -1,7 +1,10 @@ ## Correlation Method *** -💡 **Tip**: For details, visit this link. - +
+💡 Tip: For more detailed information, please visit +this page. +
+
### Methods: 1. **Pearson:** diff --git a/program/shinyApp/helpfiles/SampleCorr_Color.md b/program/shinyApp/helpfiles/SampleCorr_Color.md index 250b619f..49c86a05 100644 --- a/program/shinyApp/helpfiles/SampleCorr_Color.md +++ b/program/shinyApp/helpfiles/SampleCorr_Color.md @@ -1,7 +1,11 @@ ## Color Annotation *** -💡 **Tip**: For more detailed information, please visit here. +
+💡 Tip: For more detailed information, please visit +this page. +
+
You can choose **Multiple** options. Each option is a column from the `sample annotation table`. The clustered samples will be colored on the right side by your diff --git a/program/shinyApp/helpfiles/SampleCorr_Downloads.md b/program/shinyApp/helpfiles/SampleCorr_Downloads.md index 4932c074..abc414a1 100644 --- a/program/shinyApp/helpfiles/SampleCorr_Downloads.md +++ b/program/shinyApp/helpfiles/SampleCorr_Downloads.md @@ -1,7 +1,11 @@ ## Download Helper *** -💡 **Tip**: For more detailed information, please visit here. +
+💡 Tip: For more detailed information, please visit +this page. +
+
These buttons serve for various downloading purposes. diff --git a/program/shinyApp/helpfiles/SigAna_Choices.md b/program/shinyApp/helpfiles/SigAna_Choices.md index 049904e7..2e4de2d3 100644 --- a/program/shinyApp/helpfiles/SigAna_Choices.md +++ b/program/shinyApp/helpfiles/SigAna_Choices.md @@ -1,6 +1,9 @@ ## Significance Analysis Options - -💡 **Tip**: For more details, visit here. +
+💡 Tip: For more detailed information, please visit +this page. +
+
1. **Groups to Compare** - Select groups for significance analysis based on predefined factors (for DESeq) or sample annotations. diff --git a/program/shinyApp/helpfiles/SigAna_Intersections.md b/program/shinyApp/helpfiles/SigAna_Intersections.md index 194cd27b..1a5feb99 100644 --- a/program/shinyApp/helpfiles/SigAna_Intersections.md +++ b/program/shinyApp/helpfiles/SigAna_Intersections.md @@ -1,7 +1,11 @@ ## Highlight and Download intersections *** -💡 **Tip**: For more detailed information, please visit here. +
+💡 Tip: For more detailed information, please visit +this page. +
+
To allow for a better overview of the intersections, the user can highlight the intersections of interest. You can choose from all available intersections in the diff --git a/program/shinyApp/helpfiles/SigAna_Vis.md b/program/shinyApp/helpfiles/SigAna_Vis.md index f9533337..84cc3a60 100644 --- a/program/shinyApp/helpfiles/SigAna_Vis.md +++ b/program/shinyApp/helpfiles/SigAna_Vis.md @@ -1,7 +1,12 @@ ## Visualizing Significance Analysis Results Options *** -💡 **Tip**: For more detailed information, please visit here. +
+💡 Tip: For more detailed information, please visit +this page. +
+
+ **1. Select Comparisons to Visualize:** diff --git a/program/shinyApp/helpfiles/SingleGene_Options.md b/program/shinyApp/helpfiles/SingleGene_Options.md index 0f399eae..8fa7bee7 100644 --- a/program/shinyApp/helpfiles/SingleGene_Options.md +++ b/program/shinyApp/helpfiles/SingleGene_Options.md @@ -1,7 +1,11 @@ ## Single Gene Visualization Options --- -💡 **Tip**: For more detailed information, please visit here. +
+💡 Tip: For more detailed information, please visit +this page. +
+
**1. Choose Data Type:** diff --git a/program/shinyApp/helpfiles/SingleGene_Select.md b/program/shinyApp/helpfiles/SingleGene_Select.md index df00a86b..ffedb46f 100644 --- a/program/shinyApp/helpfiles/SingleGene_Select.md +++ b/program/shinyApp/helpfiles/SingleGene_Select.md @@ -1,7 +1,11 @@ ## Choosing groups for comparison --- -💡 **Tip**: For more detailed information, please visit here. +
+💡 Tip: For more detailed information, please visit +this page. +
+
This option lets you specify how to group the samples based on the annotation categories provided in the sample annotation file. This only has an effect if you have chosen diff --git a/program/shinyApp/helpfiles/TakingNotesMD_help.md b/program/shinyApp/helpfiles/TakingNotesMD_help.md index 0d319ba3..7bd72c0c 100644 --- a/program/shinyApp/helpfiles/TakingNotesMD_help.md +++ b/program/shinyApp/helpfiles/TakingNotesMD_help.md @@ -1,7 +1,11 @@ ## Personal Note Taking *** -💡 **Tip**: For more detailed information, please visit here. +
+💡 Tip: For more detailed information, please visit +this page. +
+
This Section is here for your Notes. It can be as easy as just a keyword or as complex as an entire figure description or even an entire book (however I do think there are better tools for this). To enable possibilities to structure your text, involving headings, bullets points or colored chunks `markdown` syntax can be used. diff --git a/program/shinyApp/helpfiles/helpTab_question.md b/program/shinyApp/helpfiles/helpTab_question.md index c6221226..3508b5be 100644 --- a/program/shinyApp/helpfiles/helpTab_question.md +++ b/program/shinyApp/helpfiles/helpTab_question.md @@ -1,6 +1,10 @@ ## Congrats! *** -💡 **Tip**: If you click here you will be directed to the correct location within the documentation. Note: Here is the beginning of the documentation. +
+💡 Tip: If you click +this page.you will be directed to the correct location within the documentation. Note: Here is the beginning of the documentation. +
+
You found your first question mark. Watch out for these to get immediate help on the particular topic the question mark is attached to. They often also direct you to further