(Nucleomics-VIB)
- Shiny-Apps
All tools presented below have only been tested by me and may contain bugs, please let me know if you find some. Each tool relies on dependencies normally listed at the top of the code (cpan for perl and cran for R will help you add them)
Please refer to the accompanying wiki for examples and workflows.
Read the header of each App.R to find out which packages you need to install on your server to have the code do its job.
A server hosting these apps is located here (you are welcome to use it but please limit your queries and file sizes)
Those additional tools belong on a Shiny server and will execute R code in a interactive manner (please refder to https://shiny.rstudio.com/ for info about Shiny).
The RNASeqFiltering.shinyapp app loads a StatisticalResults.xlsx Excel file provided by the Nucleomics Core and filters it on one or more contrasts with chosen FDR and logFC limits. It then saves the results to XLSX and text files for further use. A live version was posted to https://nucleomics-core.shinyapps.io/RNASeqFiltering/. A sample ZIP file is present in the 'Data' subfolder for your convenience (sample.zip). A bundle can be downloaded (here) to install the tool on your computer (you will need RStudio and a few R packages to run it)
The fpkm2heatmap.shinyapp app loads a FPKM Excel file provided by the Nucleomics Core and a list of EnsEMBL gene IDs (signature) and produced a heatmap plot that can be tuned to your needs. A live version was posted to https://nucleomics-core.shinyapps.io/fpkm2heatmap/. A sample ZIP file is present in the 'Data' subfolder for your convenience (sample.zip). A bundle can be downloaded (here) to install the tool on your computer (you will need RStudio and a few R packages to run it)
The RBioanalyzer.shinyapp app loads 2 to 3 Bioanalyzer exported csv files and creates an overlay plot. A live version was posted to https://nucleomics-core.shinyapps.io/RBioanalyzer/. A sample ZIP file is present in the 'Data' subfolder for your convenience (sample.zip). A bundle can be downloaded (here) to install the tool on your computer (you will need RStudio and a few R packages to run it)
The RFilterRNASeq.shinyapp app loads a StatisticalResults.xlsx file obtained from the Core, filters each contrast based on user input, and creates a Venn plot and a count table. The Venn plot supports up to 5 contrasts and is not created beyond that. A live version was posted to https://nucleomics-core.shinyapps.io/RFilterRNASeq/. A sample excel file with 2000 gene rows is present in the 'Data' subfolder for your convenience (StatisticalResults.xlsx). A bundle can be downloaded (here) to install the tool on your computer (you will need RStudio and a few R packages to run it)
The assemblyNplot.shinyapp app app plots N-graphs from a zip of fasta genome assemblies (one or more fasta files).
The multiLengthplot.shinyapp app plots length densities from a zip of text files reporting lengths (eg. lengths of fasta records or whatever length you can measure, one or more text files).
The BNX_viewer.shinyapp app loads BNX data from a file and creates scatterplots or histograms with filtering (no export at this point, one can easily use built-in functions for that purpose). A live version was posted to https://nucleomics-core.shinyapps.io/bnx_filter/ (the hosted version is size limited due to the hosting policy but accepts large BNX files when hosted on your own servzer or run locally). A sample BNX file can be downloaded from the App or here for testing.
Please send comments and feedback to [email protected]
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