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Introduction
Shiny Transcriptomic Aggregator is a web-based application designed to explore RNA-seq data. The default dataset made available here is a collection of samples for the model brown alga Ectocarpus but the application can be run with any RNA-seq dataset provided using the “import new data” function. The Ectocarpus RNA-seq data corresponds to multiple life cycle and developmental stages and to strains grown under different environmental conditions such as heat and salinity stresses.
The application consists of several tabs allowing users to easily import, analyze, visualize and explore RNA Seq data.
Some examples of Shiny Transcriptomic Aggregator graphic output are shown below.
User guide
RNAseq aggregator step by step
1 - Take a look to the sample and gene tables in the “Ectocarpus datatables” tab.
2 - Access the “Table” tab to filter Ectocarpus data.
3 - Select samples and/or genes filters and apply your selection with the “Apply filters” button.
4 - Build a plot of the filtered data in the plots tab. Plots are built from the data displayed in the table tab.
Features
Table
The table is the main part of Shiny Transcriptomic Aggregator.
It is used to analyze, visualize, explore and filter RNA Seq data.
It consists in two collapsible filter panels at the top of the page, one for sample metadata and the other for gene metadata, that are generated automatically from sample and gene file columns. Below these panels are a collapsible sample list and the table. The filter panels and the sample list allow selection and display of a subset of the table according to the filters chosen.
To apply filters, click on the “Apply filters” button in the upper right corner. This will update the table.
You can reset the filters by pressing the different reset filters buttons. Clicking on one of these buttons does not update the table. Don't forget to click on the “Apply filters” button afterwards.
The table is a dynamic overview of your data. Many features are provided such as searching, sorting or exporting for example.
Charts
3 charts are available :
| Barplot | Boxplot | Heatmap |
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Use the Visualize button to preview the generated graph. It can then be downloaded in different formats.
Optional features
Import new data
You can import a new set of data using the file browsers in the “Import new data” tab.
Genes, samples and TPM data files are required in this case and should be constructed as follows :
Genes data file (.csv)
gene_id* gene_metadata_1 gene_metadata_2 … (character) (character) (character) … gene1 value value … gene2 value value … … … … … Samples data file (.csv)
sample_id* sample_name private sample_metadata_1 sample_metadata_2 … (character) (character) (boolean) (character) (character) … sample1 name1_2 TRUE value value … sample2 name1_2 FALSE value value … … … … … … … TPMs file (.csv)
gene_id* sample1 sample2 … (character) (numeric) (numeric) … gene1 TPM TPM … gene2 TPM TPM … … … … …
(*) gene_id and sample_id should be unique
Underlined columns are required and should be named as above
Avoid using hyphens (-) in your tables, underscores (_) are OK.