From ce70fbb785ef23d9e90f78a1cd99d81bd55fb6c3 Mon Sep 17 00:00:00 2001 From: "Lea@Mac" Date: Tue, 5 Nov 2024 16:18:06 +0100 Subject: [PATCH] links now in question marks to precise location in docs --- .../shinyApp/helpfiles/DataSelection_DataUploadFileInput.md | 1 + program/shinyApp/helpfiles/DataSelection_MetaData.md | 1 + program/shinyApp/helpfiles/DataSelection_RowSelection.md | 1 + program/shinyApp/helpfiles/DataSelection_SummarizedExp.md | 1 + .../shinyApp/helpfiles/DataSelection_UploadInspection.md | 1 + program/shinyApp/helpfiles/EA_GeneSets.md | 2 ++ program/shinyApp/helpfiles/EA_Options.md | 2 ++ program/shinyApp/helpfiles/Heatmap_Aesthetics.md | 2 ++ program/shinyApp/helpfiles/Heatmap_FurtherOptions.md | 2 ++ program/shinyApp/helpfiles/Heatmap_Options.md | 6 +++--- program/shinyApp/helpfiles/Heatmap_RowAnnoBased.md | 1 + program/shinyApp/helpfiles/PCA_Choices.md | 1 + program/shinyApp/helpfiles/PreProcessing_DESeqMain.md | 3 +++ program/shinyApp/helpfiles/PreProcessing_Procedures.md | 2 ++ program/shinyApp/helpfiles/SampleCorr_Choices.md | 1 + program/shinyApp/helpfiles/SampleCorr_Color.md | 1 + program/shinyApp/helpfiles/SampleCorr_Downloads.md | 1 + program/shinyApp/helpfiles/SigAna_Choices.md | 3 +++ program/shinyApp/helpfiles/SigAna_Intersections.md | 2 ++ program/shinyApp/helpfiles/SigAna_Vis.md | 2 ++ program/shinyApp/helpfiles/SingleGene_Options.md | 2 ++ program/shinyApp/helpfiles/SingleGene_Select.md | 2 ++ program/shinyApp/helpfiles/TakingNotesMD_help.md | 2 ++ 23 files changed, 39 insertions(+), 3 deletions(-) diff --git a/program/shinyApp/helpfiles/DataSelection_DataUploadFileInput.md b/program/shinyApp/helpfiles/DataSelection_DataUploadFileInput.md index b86ad0e6..a84561ce 100644 --- a/program/shinyApp/helpfiles/DataSelection_DataUploadFileInput.md +++ b/program/shinyApp/helpfiles/DataSelection_DataUploadFileInput.md @@ -1,6 +1,7 @@ ### Data Upload via File Input *** +💡 **Tip**: For more detailed information, please visit here. 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_MetaData.md b/program/shinyApp/helpfiles/DataSelection_MetaData.md index 6c312ffa..9b5e6590 100644 --- a/program/shinyApp/helpfiles/DataSelection_MetaData.md +++ b/program/shinyApp/helpfiles/DataSelection_MetaData.md @@ -1,6 +1,7 @@ ### Data Upload via File Input + Meta Data Sheet *** +💡 **Tip**: For more detailed information, please visit here. 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 8f1db2de..693ab542 100644 --- a/program/shinyApp/helpfiles/DataSelection_RowSelection.md +++ b/program/shinyApp/helpfiles/DataSelection_RowSelection.md @@ -1,6 +1,7 @@ ### Data Selection by Columns and Rows *** +💡 **Tip**: For more detailed information, please visit here. 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 2f3d0a6c..4513c88f 100644 --- a/program/shinyApp/helpfiles/DataSelection_SummarizedExp.md +++ b/program/shinyApp/helpfiles/DataSelection_SummarizedExp.md @@ -1,6 +1,7 @@ ### Data Upload via Precompiled Data *** +💡 **Tip**: For more detailed information, please visit here. 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 a0736e63..37a83720 100644 --- a/program/shinyApp/helpfiles/DataSelection_UploadInspection.md +++ b/program/shinyApp/helpfiles/DataSelection_UploadInspection.md @@ -1,6 +1,7 @@ ### Data Quality Check - Visual Inspection *** +💡 **Tip**: For more detailed information, please visit here. 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_GeneSets.md b/program/shinyApp/helpfiles/EA_GeneSets.md index 365ff648..956976d0 100644 --- a/program/shinyApp/helpfiles/EA_GeneSets.md +++ b/program/shinyApp/helpfiles/EA_GeneSets.md @@ -1,5 +1,7 @@ ## Gene Sets for Enrichment Analysis +*** + You can choose a variety of gene sets for enrichment analysis. Here you find a description of the gene sets. The information was taken from the [MSigDB database](https://www.gsea-msigdb.org/gsea/msigdb/collections.jsp), where you diff --git a/program/shinyApp/helpfiles/EA_Options.md b/program/shinyApp/helpfiles/EA_Options.md index c07c6808..b3add8f5 100644 --- a/program/shinyApp/helpfiles/EA_Options.md +++ b/program/shinyApp/helpfiles/EA_Options.md @@ -1,6 +1,8 @@ ## Enrichment Analysis Options --- +💡 **Tip**: For more detailed information, please visit here. + 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 [Gene Set Enrichment Analysis](https://www.pnas.org/doi/abs/10.1073/pnas.0506580102) diff --git a/program/shinyApp/helpfiles/Heatmap_Aesthetics.md b/program/shinyApp/helpfiles/Heatmap_Aesthetics.md index 7dba6151..925756ca 100644 --- a/program/shinyApp/helpfiles/Heatmap_Aesthetics.md +++ b/program/shinyApp/helpfiles/Heatmap_Aesthetics.md @@ -1,6 +1,8 @@ ## Heatmap Aesthetics Options --- +💡 **Tip**: For more detailed information, please visit here. + **1. Choose Variable to Color the Samples After:** - **Description:** diff --git a/program/shinyApp/helpfiles/Heatmap_FurtherOptions.md b/program/shinyApp/helpfiles/Heatmap_FurtherOptions.md index d23fa082..df46e599 100644 --- a/program/shinyApp/helpfiles/Heatmap_FurtherOptions.md +++ b/program/shinyApp/helpfiles/Heatmap_FurtherOptions.md @@ -1,6 +1,8 @@ ## Log Fold Change (LFC) Ordering Options *** +💡 **Tip**: For more detailed information, please visit here. + **1. Choose Type for LFC-Based Ordering:** - **Description:** diff --git a/program/shinyApp/helpfiles/Heatmap_Options.md b/program/shinyApp/helpfiles/Heatmap_Options.md index d7315ff7..eb030662 100644 --- a/program/shinyApp/helpfiles/Heatmap_Options.md +++ b/program/shinyApp/helpfiles/Heatmap_Options.md @@ -1,8 +1,8 @@ - ---- - ## Row Selection Options +*** +💡 **Tip**: For more detailed information, please visit here. + **1. Row Selection Options:** - **Description** diff --git a/program/shinyApp/helpfiles/Heatmap_RowAnnoBased.md b/program/shinyApp/helpfiles/Heatmap_RowAnnoBased.md index 00ac4d3f..dba09f13 100644 --- a/program/shinyApp/helpfiles/Heatmap_RowAnnoBased.md +++ b/program/shinyApp/helpfiles/Heatmap_RowAnnoBased.md @@ -1,6 +1,7 @@ ## Additional Row Selection Options --- +💡 **Tip**: For more detailed information, please visit here. 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 89316e70..2b58680a 100644 --- a/program/shinyApp/helpfiles/PCA_Choices.md +++ b/program/shinyApp/helpfiles/PCA_Choices.md @@ -1,6 +1,7 @@ ## Principal Component Analysis (PCA) Options *** +💡 **Tip**: For more detailed information, please visit here. 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_DESeqMain.md b/program/shinyApp/helpfiles/PreProcessing_DESeqMain.md index 8de88264..08f6317b 100644 --- a/program/shinyApp/helpfiles/PreProcessing_DESeqMain.md +++ b/program/shinyApp/helpfiles/PreProcessing_DESeqMain.md @@ -1,5 +1,8 @@ ## DESeq Factor Choices +*** +💡 **Tip**: For more detailed information, please visit here. + ### Understanding the Design Matrix in DESeq2 The design matrix in DESeq2 is a fundamental component used to specify the experimental design of your RNA-seq dataset. It helps in determining the relationship between the observed counts and the experimental conditions. Here's a detailed explanation: diff --git a/program/shinyApp/helpfiles/PreProcessing_Procedures.md b/program/shinyApp/helpfiles/PreProcessing_Procedures.md index 2577a6cf..df7aa317 100644 --- a/program/shinyApp/helpfiles/PreProcessing_Procedures.md +++ b/program/shinyApp/helpfiles/PreProcessing_Procedures.md @@ -1,4 +1,6 @@ ## Data Preprocessing +*** +💡 **Tip**: For more detailed information, please visit here. **Step 1: General Data Cleaning** diff --git a/program/shinyApp/helpfiles/SampleCorr_Choices.md b/program/shinyApp/helpfiles/SampleCorr_Choices.md index bc2b6c8e..7b119e8b 100644 --- a/program/shinyApp/helpfiles/SampleCorr_Choices.md +++ b/program/shinyApp/helpfiles/SampleCorr_Choices.md @@ -1,6 +1,7 @@ ## Correlation method *** +💡 **Tip**: For more detailed information, please visit here. Choose **one** of the following correlation methods. These correlation methods provide insights into different aspects of relationships between variables. Understanding diff --git a/program/shinyApp/helpfiles/SampleCorr_Color.md b/program/shinyApp/helpfiles/SampleCorr_Color.md index a051f932..c16fa551 100644 --- a/program/shinyApp/helpfiles/SampleCorr_Color.md +++ b/program/shinyApp/helpfiles/SampleCorr_Color.md @@ -1,6 +1,7 @@ ## Color Annotation *** +💡 **Tip**: For more detailed information, please visit here. 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 78f179f2..4932c074 100644 --- a/program/shinyApp/helpfiles/SampleCorr_Downloads.md +++ b/program/shinyApp/helpfiles/SampleCorr_Downloads.md @@ -1,6 +1,7 @@ ## Download Helper *** +💡 **Tip**: For more detailed information, please visit here. These buttons serve for various downloading purposes. diff --git a/program/shinyApp/helpfiles/SigAna_Choices.md b/program/shinyApp/helpfiles/SigAna_Choices.md index 2e0f2e43..5228bd92 100644 --- a/program/shinyApp/helpfiles/SigAna_Choices.md +++ b/program/shinyApp/helpfiles/SigAna_Choices.md @@ -1,5 +1,8 @@ ## Significance Analysis Options +*** +💡 **Tip**: For more detailed information, please visit here. + **1. Choose Groups to Compare:** - **Description:** diff --git a/program/shinyApp/helpfiles/SigAna_Intersections.md b/program/shinyApp/helpfiles/SigAna_Intersections.md index f776b11f..29833cbd 100644 --- a/program/shinyApp/helpfiles/SigAna_Intersections.md +++ b/program/shinyApp/helpfiles/SigAna_Intersections.md @@ -1,6 +1,8 @@ ## Highlight and Download intersections *** +💡 **Tip**: For more detailed information, please visit here. + 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 `Intersections to highlight` menu. The intersection names shown in the Upset plot above, diff --git a/program/shinyApp/helpfiles/SigAna_Vis.md b/program/shinyApp/helpfiles/SigAna_Vis.md index d1126b15..a4320a45 100644 --- a/program/shinyApp/helpfiles/SigAna_Vis.md +++ b/program/shinyApp/helpfiles/SigAna_Vis.md @@ -1,6 +1,8 @@ ## Visualizing Significance Analysis Results Options *** +💡 **Tip**: For more detailed information, please visit here. + **1. Select Comparisons to Visualize:** - **Description:** diff --git a/program/shinyApp/helpfiles/SingleGene_Options.md b/program/shinyApp/helpfiles/SingleGene_Options.md index f3bfad2a..8b918445 100644 --- a/program/shinyApp/helpfiles/SingleGene_Options.md +++ b/program/shinyApp/helpfiles/SingleGene_Options.md @@ -1,6 +1,8 @@ ## Single Gene Visualization Options --- +💡 **Tip**: For more detailed information, please visit here. + **1. Choose Data Type:** - **Description:** diff --git a/program/shinyApp/helpfiles/SingleGene_Select.md b/program/shinyApp/helpfiles/SingleGene_Select.md index ec36db10..024c79d5 100644 --- a/program/shinyApp/helpfiles/SingleGene_Select.md +++ b/program/shinyApp/helpfiles/SingleGene_Select.md @@ -1,6 +1,8 @@ ## Choosing groups for comparison --- +💡 **Tip**: For more detailed information, please visit here. + 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 `boxplots_withTesting` as the visualization style. diff --git a/program/shinyApp/helpfiles/TakingNotesMD_help.md b/program/shinyApp/helpfiles/TakingNotesMD_help.md index 7deceae8..0d319ba3 100644 --- a/program/shinyApp/helpfiles/TakingNotesMD_help.md +++ b/program/shinyApp/helpfiles/TakingNotesMD_help.md @@ -1,5 +1,7 @@ ## Personal Note Taking +*** +💡 **Tip**: For more detailed information, please visit here. 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.