diff --git a/docs/_data/navigation.yml b/docs/_data/navigation.yml index dc678eaa..ded86898 100644 --- a/docs/_data/navigation.yml +++ b/docs/_data/navigation.yml @@ -4,22 +4,24 @@ main: - title: "Interface Details" url: "/interface-details/" children: + - title: "Data Input" + url: "/interface-details/01-required-data-input/" - title: "Data selection" - url: "/interface-details/selection/" + url: "/interface-details/02-selection/" - title: "Pre-processing" - url: "/interface-details/pre-processing/" + url: "/interface-details/03-pre-processing/" - title: "Sample Correlation" - url: "/interface-details/sample-correlation/" + url: "/interface-details/04-sample-correlation/" - title: "Significance Analysis" - url: "/interface-details/significance-analysis/" + url: "/interface-details/05-significance-analysis/" - title: "PCA" - url: "/interface-details/pca/" + url: "/interface-details/06-pca/" - title: "Heatmap" - url: "/interface-details/heatmap/" + url: "/interface-details/07-heatmap/" - title: "Single Gene Visualisations" - url: "/interface-details/single-gene-visualisations/" + url: "/interface-details/08-single-gene-visualisations/" - title: "Enrichment Analysis" - url: "/interface-details/enrichment-analysis/" + url: "/interface-details/09-enrichment-analysis/" - title: "Local installation" url: "/installation/" - title: "Using provided R Code and Data" diff --git a/docs/index.md b/docs/index.md index 0e36b9fe..6d9be167 100644 --- a/docs/index.md +++ b/docs/index.md @@ -18,7 +18,7 @@ Have fun exploring! πŸŽ‰ ### Quick Links to Get You Started: -- πŸ“š Want to know the required data and format? Visit [Interface Details](interface-details/required-data-input.md). +- πŸ“š Want to know the required data and format? Visit [Interface Details](interface-details/01-required-data-input.md). - πŸ”§ Need to run the app locally? Check out the [Installation Guide](installation.md). - πŸ’‘ Looking for customization inspiration? Explore our [Customization Examples](code-and-data/examples.md). -- πŸ“Š Want to know more about the significance analysis? Visit [Significance Analysis](interface-details/significance-analysis.md) +- πŸ“Š Want to know more about the significance analysis? Visit [Significance Analysis](interface-details/05-significance-analysis.md) diff --git a/docs/interface-details.md b/docs/interface-details.md index 38c24d00..8bb3095b 100644 --- a/docs/interface-details.md +++ b/docs/interface-details.md @@ -50,6 +50,3 @@ To get more information on the tabs, navigate to the respective documentation us 5. **Get Underlying R Code and Data:** Upon button click, the R script and respective data to generate the shown plot will be available for download. The script includes data selection, preprocessing, and analysis. For more details, refer to [Code and Data](code-and-data.md). 6. **Notes:** At the bottom of each tab, there is a Notes field where you can enter text that will be saved within the report. You can use [markdown syntax](https://www.markdownguide.org/cheat-sheet/) here. - - - diff --git a/docs/interface-details/required-data-input.md b/docs/interface-details/01-required-data-input.md similarity index 89% rename from docs/interface-details/required-data-input.md rename to docs/interface-details/01-required-data-input.md index 80a2dc4c..b93f7338 100644 --- a/docs/interface-details/required-data-input.md +++ b/docs/interface-details/01-required-data-input.md @@ -5,7 +5,6 @@ parent: Interface Details nav_order: 1 --- - # The Very Start πŸš€ To start your own analysis, you need to pass the first hurdle - Uploading your data. (Note: If you want to check out what the app is capable of, you might want to use the Test data. For detailed instructions, check out [Interface Details](interface-details/selection.md)). @@ -29,12 +28,12 @@ When you have only your omics data table (referred to as the Data Matrix), ensur ### Creating a Sample Table πŸ”§ Having the data matrix, you need to create a fitting Sample table.πŸ–‡οΈ A fitting sample table has the column names of the data matrix in its row names. Each additional column in the sample table carries additional information about the samples (referred to as sample annotation). Examples are condition, height, or phenotype. You are not limited to the number of columns, hence to the number of information you can supply to your samples. -Within cOmicsART, this information is used, for example, to perform batch correction, data selection, or to visualize respective groups of samples. If this sounds confusing, don't worry - it becomes clearer throughout usage and this documentation. Make sure to check out the [data selection](selection.md) to see how your sample data is utilized in the data selection process. +Within cOmicsART, this information is used, for example, to perform batch correction, data selection, or to visualize respective groups of samples. If this sounds confusing, don't worry - it becomes clearer throughout usage and this documentation. Make sure to check out the [data selection](02-selection.md) to see how your sample data is utilized in the data selection process. ### Creating an Annotation Table πŸ”§ Having the data matrix, you need to create a fitting annotation table.πŸ–‡οΈ A fitting annotation table has the row names of the data matrix in its row names. Each additional column in the annotation table carries additional information about the entities (referred to as row annotation). Examples are gene type, lipid class, or other IDs. You are not limited to the number of columns, hence to the number of information you can supply to your entities. -Within cOmicsART, this information can be used within the data selection or to be visualized instead of the row index. For some examples of the data selection, go to [data selection](selection.md). +Within cOmicsART, this information can be used within the data selection or to be visualized instead of the row index. For some examples of the data selection, go to [data selection](02-selection.md). ### All in Short 🎁 The files must be in the following format:
@@ -67,8 +66,24 @@ The Metadatasheet enables biomedical researchers to organize their data and meta ### Creating an Annotation Table πŸ”§ Having the data matrix, you need to create a fitting annotation table. A fitting annotation table has the row names of the data matrix in its row names. Each additional column in the annotation table carries additional information about the entities (referred to as row annotation). Examples are gene type, lipid class, or other IDs. You are not limited to the number of columns, hence to the number of information you can supply to your entities. -Within cOmicsArt, this information can be used within the data selection or to be visualized instead of the row index. For some examples of the data selection, go to [data selection](selection.md). +Within cOmicsArt, this information can be used within the data selection or to be visualized instead of the row index. For some examples of the data selection, go to [data selection](02-selection.md). ## Starting with an RDS Object -Once you have uploaded your three data tables to the app, you can click on 'save as RDS Object'. This is an R-specific object that saves all three files in one object. Hence, for any new analysis, you can just upload this single file and not multiple to save yourself some time. Note that the RDS object is in general not a standardardized format, which means that you cannot upload any RDS object. +Once you have uploaded your three data tables to the app, you can click on 'save as RDS Object'. This is an R-specific object that saves all three files in one object. Hence, for any new analysis, you can just upload this single file and not multiple to save yourself some time. Note that the RDS object is in general not a standardardized format, which means that you cannot upload any RDS object. + +--- + +## Further Navigation +Do you want to... + +- Understand how to select and filter your data? β†’ Go to [Data selection](02-selection.md) +- Discover the pre-processing options available? β†’ Go to [Pre-processing](03-pre-processing.md) +- Explore how to correlate your samples? β†’ Go to [Sample Correlation](04-sample-correlation.md) +- Perform significance analysis on your data? β†’ Go to [Significance Analysis](05-significance-analysis.md) +- Conduct Principal Component Analysis? β†’ Go to [PCA](06-pca.md) +- Visualize your data with heatmaps? β†’ Go to [Heatmap](07-heatmap.md) +- Visualize individual genes? β†’ Go to [Single Gene Visualisations](08-single-gene-visualisations.md) +- Perform enrichment analysis on your data? β†’ Go to [Enrichment Analysis](09-enrichment-analysis.md) + +--- diff --git a/docs/interface-details/selection.md b/docs/interface-details/02-selection.md similarity index 81% rename from docs/interface-details/selection.md rename to docs/interface-details/02-selection.md index 15087a7a..184c61dc 100644 --- a/docs/interface-details/selection.md +++ b/docs/interface-details/02-selection.md @@ -2,7 +2,7 @@ title: "Data Selection" layout: default parent: Interface Details -nav_order: 1 +nav_order: 2 --- # Data Selection @@ -12,7 +12,7 @@ The Data Selection tab is the initial step to upload and manage your data in cOm ## Side Panel πŸ“š The side panel offers several tabs for different data input methods. The data Upload -and possible structure are detailed in the [Data Input](required-data-input.md). +and possible structure are detailed in the [Data Input](01-required-data-input.md). Nonetheless, here is a short overview: ### File Input πŸ› οΈ @@ -95,8 +95,25 @@ The main panel provides options for detailed data selection: ### Start the Journey πŸš€ - **Start the Journey**: Click this button to proceed with the analysis. This will - automatically bring you to the [Pre-processing tab](pre-processing.md). + automatically bring you to the [Pre-processing tab](03-pre-processing.md). ### Other Notes πŸ“Œ - **Question Marks**: The displayed question marks provide quick and immediate help. They offer guidance and additional information about the options available. + +--- + +## Further Navigation + +Do you want to... + +- Learn how to upload your data? β†’ Go to [Data Input](01-required-data-input.md) +- Discover the pre-processing options available? β†’ Go to [Pre-processing](03-pre-processing.md) +- Explore how to correlate your samples? β†’ Go to [Sample Correlation](04-sample-correlation.md) +- Perform significance analysis on your data? β†’ Go to [Significance Analysis](05-significance-analysis.md) +- Conduct Principal Component Analysis? β†’ Go to [PCA](06-pca.md) +- Visualize your data with heatmaps? β†’ Go to [Heatmap](07-heatmap.md) +- Visualize individual genes? β†’ Go to [Single Gene Visualisations](08-single-gene-visualisations.md) +- Perform enrichment analysis on your data? β†’ Go to [Enrichment Analysis](09-enrichment-analysis.md) + +--- diff --git a/docs/interface-details/pre-processing.md b/docs/interface-details/03-pre-processing.md similarity index 61% rename from docs/interface-details/pre-processing.md rename to docs/interface-details/03-pre-processing.md index 01c09297..4853f585 100644 --- a/docs/interface-details/pre-processing.md +++ b/docs/interface-details/03-pre-processing.md @@ -2,7 +2,7 @@ title: "Pre-processing" layout: default parent: "Interface Details" -nav_order: 4 +nav_order: 3 --- # Pre-processing @@ -18,7 +18,11 @@ In the side panel, you have the following options: - Options: none, filterOnly, vst_DESeq, simpleCenterScaling, Scaling_0_1, log10, log2, pareto_scaling, ln - vst_DESeq also requires the selection of a design formula. -- **Select Batch Effect Column**: Choose a batch effect if applicable. Possible choices are taken from the sample annotation columns. +- **Select Batch Effect Column**: Choose a batch effect if applicable. Possible + choices are taken from the sample annotation columns. **Important**: This step is + optional, as sometimes no batches need to be accounted for. Additionally, in the + very first run, batch effects might not be know, thus using no batch effects and + looking at correlations and PCA plots can help to identify them. - **Get Pre-Processing**: Clicking this button will apply the selected pre-processing procedure to the data. @@ -40,3 +44,20 @@ The main panel displays the results of the pre-processing. Here are some key poi - **Question Marks**: The displayed question marks provide quick and immediate help. However, since you are reading this documentation, you found the extensive version. Hope it helped! - **Pre-processing Interpretation**: Observing the pre-processed data can provide insights into how different pre-processing procedures affect the data. Adjusting the pre-processing parameters can help in optimizing the data for downstream analyses. + +--- + +## Further Navigation + +Do you want to... + +- Learn how to upload your data? β†’ Go to [Data Input](01-required-data-input.md) +- Understand how to select and filter your data? β†’ Go to [Data selection](02-selection.md) +- Explore how to correlate your samples? β†’ Go to [Sample Correlation](04-sample-correlation.md) +- Perform significance analysis on your data? β†’ Go to [Significance Analysis](05-significance-analysis.md) +- Conduct Principal Component Analysis? β†’ Go to [PCA](06-pca.md) +- Visualize your data with heatmaps? β†’ Go to [Heatmap](07-heatmap.md) +- Visualize individual genes? β†’ Go to [Single Gene Visualisations](08-single-gene-visualisations.md) +- Perform enrichment analysis on your data? β†’ Go to [Enrichment Analysis](09-enrichment-analysis.md) + +--- diff --git a/docs/interface-details/sample-correlation.md b/docs/interface-details/04-sample-correlation.md similarity index 73% rename from docs/interface-details/sample-correlation.md rename to docs/interface-details/04-sample-correlation.md index 26511992..21a5c157 100644 --- a/docs/interface-details/sample-correlation.md +++ b/docs/interface-details/04-sample-correlation.md @@ -2,7 +2,7 @@ title: "Sample Correlation" layout: default parent: Interface Details -nav_order: 3 +nav_order: 4 --- # Sample Correlation @@ -24,7 +24,7 @@ In the side panel, you have the following options: - **Choose the color annotation for the samples**: Below the horizontal line, you can choose different options to color the rows. These options come from the sample annotations provided initially. This can help to potentially explain clustering behavior observed in the heatmap. - More details on these options can be found under [Required Data Input](required-data-input.md) or [Showcase A](../showcases/showcase-a.md). + More details on these options can be found under [Required Data Input](01-required-data-input.md) or [Showcase A](../showcases/showcase-a.md). ## Main Panel πŸ’‘ @@ -40,3 +40,20 @@ The main panel displays the correlation heatmap. Here are some key points: - **Question Marks**: The displayed question marks provide quick and immediate help. However, since you are reading this documentation, you found the extensive version. Hope it helped! - **Clustering Behavior**: Observing the clustering in the heatmap can give insights into the relationships between different samples based on the selected annotation. +--- + +## Further Navigation + +Do you want to... + +- Learn how to upload your data? β†’ Go to [Data Input](01-required-data-input.md) +- Understand how to select and filter your data? β†’ Go to [Data selection](02-selection.md) +- Discover the pre-processing options available? β†’ Go to [Pre-processing](03-pre-processing.md) +- Perform significance analysis on your data? β†’ Go to [Significance Analysis](05-significance-analysis.md) +- Conduct Principal Component Analysis? β†’ Go to [PCA](06-pca.md) +- Visualize your data with heatmaps? β†’ Go to [Heatmap](07-heatmap.md) +- Visualize individual genes? β†’ Go to [Single Gene Visualisations](08-single-gene-visualisations.md) +- Perform enrichment analysis on your data? β†’ Go to [Enrichment Analysis](09-enrichment-analysis.md) + +--- + diff --git a/docs/interface-details/significance-analysis.md b/docs/interface-details/05-significance-analysis.md similarity index 84% rename from docs/interface-details/significance-analysis.md rename to docs/interface-details/05-significance-analysis.md index 92d33ecb..e34896ff 100644 --- a/docs/interface-details/significance-analysis.md +++ b/docs/interface-details/05-significance-analysis.md @@ -2,7 +2,7 @@ title: "Significance Analysis" layout: default parent: Interface Details -nav_order: 4 +nav_order: 5 --- # Significance Analysis @@ -20,7 +20,7 @@ In the side panel, you have the following options: - **Test method**: You can select the statistical test method to use. You can choose between [T-test](https://en.wikipedia.org/wiki/Student%27s_t-test), [Wilcoxon Rank Sum Test](https://en.wikipedia.org/wiki/Mann–Whitney_U_test), and [Welch's T-test](https://en.wikipedia.org/wiki/Welch%27s_t-test). - If you used `vst_DESeq` as the [preprocessing method](pre-processing.md), DESeq2 + If you used `vst_DESeq` as the [preprocessing method](03-pre-processing.md), DESeq2 will use the [Wald test](https://en.wikipedia.org/wiki/Wald_test). - **Significance level**: This slider allows you to set the significance level for the analysis, ranging from 0.005 to 0.1. @@ -72,3 +72,20 @@ The main panel displays the results of the significance analysis. The main panel changes between the compared groups. Adjusting the significance level and thresholds can help in identifying the most relevant results. Checking the intersections can point towards commonalities between the groups. + +--- + +## Further Navigation + +Do you want to... + +- Learn how to upload your data? β†’ Go to [Data Input](01-required-data-input.md) +- Understand how to select and filter your data? β†’ Go to [Data selection](02-selection.md) +- Discover the pre-processing options available? β†’ Go to [Pre-processing](03-pre-processing.md) +- Explore how to correlate your samples? β†’ Go to [Sample Correlation](04-sample-correlation.md) +- Conduct Principal Component Analysis? β†’ Go to [PCA](06-pca.md) +- Visualize your data with heatmaps? β†’ Go to [Heatmap](07-heatmap.md) +- Visualize individual genes? β†’ Go to [Single Gene Visualisations](08-single-gene-visualisations.md) +- Perform enrichment analysis on your data? β†’ Go to [Enrichment Analysis](09-enrichment-analysis.md) + +--- diff --git a/docs/interface-details/pca.md b/docs/interface-details/06-pca.md similarity index 83% rename from docs/interface-details/pca.md rename to docs/interface-details/06-pca.md index b882b23b..23c62c88 100644 --- a/docs/interface-details/pca.md +++ b/docs/interface-details/06-pca.md @@ -2,7 +2,7 @@ title: "PCA" layout: default parent: "Interface Details" -nav_order: 5 +nav_order: 6 --- # PCA @@ -48,3 +48,20 @@ The main panel displays the PCA results. Here are some key points: - **Question Marks**: The displayed question marks provide quick and immediate help. However, since you are reading this documentation, you found the extensive version. Hope it helped! - **PCA Interpretation**: Observing the PCA plot can give insights into the relationships between different samples based on the selected annotation and the principal components chosen for the axes. For more information on PCA interpretation, check out [this video on PCA interpretation](https://www.youtube.com/watch?v=FgakZw6K1QQ). +--- + +## Further Navigation + +Do you want to... + +- Learn how to upload your data? β†’ Go to [Data Input](01-required-data-input.md) +- Understand how to select and filter your data? β†’ Go to [Data selection](02-selection.md) +- Discover the pre-processing options available? β†’ Go to [Pre-processing](03-pre-processing.md) +- Explore how to correlate your samples? β†’ Go to [Sample Correlation](04-sample-correlation.md) +- Perform significance analysis on your data? β†’ Go to [Significance Analysis](05-significance-analysis.md) +- Visualize your data with heatmaps? β†’ Go to [Heatmap](07-heatmap.md) +- Visualize individual genes? β†’ Go to [Single Gene Visualisations](08-single-gene-visualisations.md) +- Perform enrichment analysis on your data? β†’ Go to [Enrichment Analysis](09-enrichment-analysis.md) + +--- + diff --git a/docs/interface-details/heatmap.md b/docs/interface-details/07-heatmap.md similarity index 80% rename from docs/interface-details/heatmap.md rename to docs/interface-details/07-heatmap.md index 2ec1e1ff..d9f13375 100644 --- a/docs/interface-details/heatmap.md +++ b/docs/interface-details/07-heatmap.md @@ -2,7 +2,7 @@ title: "Heatmap" layout: default parent: Interface Details -nav_order: 6 +nav_order: 7 --- # Heatmap @@ -16,7 +16,7 @@ Within the side panel, you have multiple options, which depend on the selected o - **Use batch corrected data?**: Allows you to choose whether to use batch corrected data. - Options: Yes, No. Note, this option only shows up at the top if you have done batch correction - within the [Pre-procesing tab](pre-processing.md) tab + within the [Pre-procesing tab](03-pre-processing.md) tab - **Select Entities to show**: Allows you to select which entities to show in the heatmap. - Options: all, Select based on Annotation, Top K. Below you can find further information. Note, that you will get a warning if you want to visualise more than 100 entries to prevent unintentional long loading times. @@ -72,7 +72,7 @@ The main panel displays the heatmap and additional options. Here are some key po will be hidden. - **Save genes shown in Heatmap for OA with Enrichment Analysis tab**: Sends the list of genes displayed in the - heatmap for further usage in the [Enrichment Analysis](enrichment-analysis.md). Hence, if one wants to send a specific set to the over-represententation analysis (OA) tab, this is the way to go. + heatmap for further usage in the [Enrichment Analysis](09-enrichment-analysis.md). Hence, if one wants to send a specific set to the over-represententation analysis (OA) tab, this is the way to go. - **Download Options**: The visualization can be downloaded directly in common formats (e.g., PNG, TIFF, PDF) or sent to the report. You can also download the underlying R code and data. For more information, check out [Interface Details](../interface-details.md). @@ -82,3 +82,20 @@ The main panel displays the heatmap and additional options. Here are some key po - **Question Marks**: The displayed question marks provide quick and immediate help. However, since you are reading this documentation, you found the extensive version. Hope it helped! - **Interpretation**: The heatmap can provide insights into the relationships between different entities based on the selected annotations and clustering options. Adjusting the selection and aesthetic parameters can help in identifying the most relevant patterns. + +--- + +## Further Navigation + +Do you want to... + +- Learn how to upload your data? β†’ Go to [Data Input](01-required-data-input.md) +- Understand how to select and filter your data? β†’ Go to [Data selection](02-selection.md) +- Discover the pre-processing options available? β†’ Go to [Pre-processing](03-pre-processing.md) +- Explore how to correlate your samples? β†’ Go to [Sample Correlation](04-sample-correlation.md) +- Perform significance analysis on your data? β†’ Go to [Significance Analysis](05-significance-analysis.md) +- Conduct Principal Component Analysis? β†’ Go to [PCA](06-pca.md) +- Visualize individual genes? β†’ Go to [Single Gene Visualisations](08-single-gene-visualisations.md) +- Perform enrichment analysis on your data? β†’ Go to [Enrichment Analysis](09-enrichment-analysis.md) + +--- diff --git a/docs/interface-details/single-gene-visualisations.md b/docs/interface-details/08-single-gene-visualisations.md similarity index 79% rename from docs/interface-details/single-gene-visualisations.md rename to docs/interface-details/08-single-gene-visualisations.md index e875d63f..be21948b 100644 --- a/docs/interface-details/single-gene-visualisations.md +++ b/docs/interface-details/08-single-gene-visualisations.md @@ -2,7 +2,7 @@ title: "Single Gene Visualisations" layout: default parent: Interface Details -nav_order: 7 +nav_order: 8 --- @@ -31,7 +31,7 @@ In the side panel, you have the following options: The main panel displays the single gene visualisations. Here are some key points: - **Visualisation**: The visualisation provides a boxplot or dot plot based on the number of samples per group and the selected options. Note that you only see boxplots if you have more than 3 samples per group. If there are fewer than 4 samples, only dots will be displayed. -- **Select your desired comparisons**: Here you select which comparisons you want to test and display in the plot. Note that each test is taken as an individual test, there is no multiple testing correction done \([Why it is important](https://www.nature.com/articles/nbt1209-1135)\) when choosing more than one test. For more advanced testing please go to the [Significance analysis tab](significance-analysis.md) +- **Select your desired comparisons**: Here you select which comparisons you want to test and display in the plot. Note that each test is taken as an individual test, there is no multiple testing correction done \([Why it is important](https://www.nature.com/articles/nbt1209-1135)\) when choosing more than one test. For more advanced testing please go to the [Significance analysis tab](05-significance-analysis.md) - **Download Options**: The visualisation can be downloaded directly in common formats (e.g., PNG, TIFF, PDF) or sent to the report. You can also download the underlying R code and data. For more information, check out [Interface Details](../interface-details.md). @@ -39,3 +39,20 @@ The main panel displays the single gene visualisations. Here are some key points ### Other Notes πŸ“Œ - **Question Marks**: The displayed question marks provide quick and immediate help. However, since you are reading this documentation, you found the extensive version. Hope it helped! + +--- + +## Further Navigation + +Do you want to... + +- Learn how to upload your data? β†’ Go to [Data Input](01-required-data-input.md) +- Understand how to select and filter your data? β†’ Go to [Data selection](02-selection.md) +- Discover the pre-processing options available? β†’ Go to [Pre-processing](03-pre-processing.md) +- Explore how to correlate your samples? β†’ Go to [Sample Correlation](04-sample-correlation.md) +- Perform significance analysis on your data? β†’ Go to [Significance Analysis](05-significance-analysis.md) +- Conduct Principal Component Analysis? β†’ Go to [PCA](06-pca.md) +- Visualize your data with heatmaps? β†’ Go to [Heatmap](07-heatmap.md) +- Perform enrichment analysis on your data? β†’ Go to [Enrichment Analysis](09-enrichment-analysis.md) + +--- diff --git a/docs/interface-details/enrichment-analysis.md b/docs/interface-details/09-enrichment-analysis.md similarity index 82% rename from docs/interface-details/enrichment-analysis.md rename to docs/interface-details/09-enrichment-analysis.md index 7b055d8d..cf86c2d2 100644 --- a/docs/interface-details/enrichment-analysis.md +++ b/docs/interface-details/09-enrichment-analysis.md @@ -2,7 +2,7 @@ title: "Enrichment Analysis" layout: default parent: Interface Details -nav_order: 8 +nav_order: 9 --- # Enrichment Analysis @@ -14,7 +14,7 @@ The Enrichment Analysis tab allows you to perform enrichment analysis specifical In the side panel, you have the following options: - **Choose an organism**: If you haven't added annotation in the [initial data - selection](selection.md), you may choose the organism your data stems from. This is + selection](02-selection.md), you may choose the organism your data stems from. This is necessary for correct data translation. - **Choose type of Analysis**: You can choose between Gene Set Enrichment (GSEA) and @@ -43,7 +43,7 @@ In the side panel, you have the following options: own** genes from data, before or after preprocessing. - **Choose a gene set to hand over to enrich**: either you provide your own set, in which case you will be asked to **select a file** or you can use genes that you - have previously used in the [heatmap tab](heatmap.md). Keep in mind however, that + have previously used in the [heatmap tab](07-heatmap.md). Keep in mind however, that you need to have sent it over with the `Save genes shown in Heatmap as list`-button. In both cases GSEA and ORA, you will have the following additional options: @@ -80,3 +80,20 @@ The main panel displays the results of the enrichment analysis. Here are some ke - **Structure Notes**: For structural reasons, it is recommended to start with Heading Level 4 (e.g., #### My personal Title). +--- + +## Further Navigation + +Do you want to... + +- Learn how to upload your data? β†’ Go to [Data Input](01-required-data-input.md) +- Understand how to select and filter your data? β†’ Go to [Data selection](02-selection.md) +- Discover the pre-processing options available? β†’ Go to [Pre-processing](03-pre-processing.md) +- Explore how to correlate your samples? β†’ Go to [Sample Correlation](04-sample-correlation.md) +- Perform significance analysis on your data? β†’ Go to [Significance Analysis](05-significance-analysis.md) +- Conduct Principal Component Analysis? β†’ Go to [PCA](06-pca.md) +- Visualize your data with heatmaps? β†’ Go to [Heatmap](07-heatmap.md) +- Visualize individual genes? β†’ Go to [Single Gene Visualisations](08-single-gene-visualisations.md) + +--- + diff --git a/docs/screen_recording.md b/docs/screen_recording.md index c0bc6200..f1fd5885 100644 --- a/docs/screen_recording.md +++ b/docs/screen_recording.md @@ -1,15 +1,21 @@ --- -title: "Screenrecording" +title: "Video Tutorial" layout: default nav_order: 8 --- ![A comic about a cat finding cOmicsART](/cOmicsArt/assets/images/cOmicsRabbit.png) *Image generated using DALL-E by OpenAI. Adjusted by Lea Seep* -# Screenrecording πŸŽ₯ +# Video Tutorial πŸŽ₯ We’ve created a detailed screen recording to guide you through the navigation of cOmicsArt. This video covers all available panels, highlighting the most crucial elements to help you to get started. +πŸ‘‰ [Watch the video here on YouTube](https://www.youtube.com/watch?v=pTGjtIYQOak) + + + ✨ To make your journey even smoother, we’ve provided time stamps below so you can jump directly to the steps that interest you the most: - [00:00](https://www.youtube.com/watch?v=pTGjtIYQOak&t=0s) Introduction @@ -26,10 +32,12 @@ We’ve created a detailed screen recording to guide you through the navigation We hope this helps you navigate cOmicsArt with ease! 😊 -πŸ‘‰ [Watch the video here on YouTube](https://www.youtube.com/watch?v=pTGjtIYQOak) - (Note, the timestamps are also given within the video description) - +## Written Tutorial πŸ“ + +Are you not a friend of video tutorials? No worries! We have two written showcases for +you. [Showcase A](../showcases/showcase-a.md) and [Showcase B](../showcases/showcase-b.md) +will guide you through the main functionalities of cOmicsArt along a real-life example. diff --git a/docs/welcome.md b/docs/welcome.md index 5a75089b..42826c43 100644 --- a/docs/welcome.md +++ b/docs/welcome.md @@ -17,7 +17,7 @@ Otherwise, you can navigate through the documentation using the sidebar on the l ### Quick Links to Get You Started: -- πŸ“š Want to know the required data and format? Visit [Interface Details](interface-details/required-data-input.md). +- πŸ“š Want to know the required data and format? Visit [Interface Details](interface-details/01-required-data-input.md). - πŸ”§ Need to run the app locally? Check out the [Installation Guide](installation.md). - πŸ’‘ Looking for customization inspiration? Explore our [Customization Examples](code-and-data/examples.md). -- πŸ“Š Want to know more about the significance analysis? Visit [Significance Analysis](interface-details/significance-analysis.md) \ No newline at end of file +- πŸ“Š Want to know more about the significance analysis? Visit [Significance Analysis](interface-details/05-significance-analysis.md) \ No newline at end of file