Academisch Medisch Centrum, Amsterdam
Stage-onderwerp 1 banaba bio-informatica 2015-2016: Evaluation of pseudo-alignment based RNA-Seq quantification
Stage-onderwerp 2 banaba bio-informatica 2015-2016: Breast cancer prognosis using H3K27ac ChIP-Seq data
Currently, at the Bioinformatics Laboratory of the Academic Medical Center, Powerpoint is used to make a report of the analysis. This presentation contains all the relevant plots and links to reports from tools in R. The layout and content of this PowerPoint, however, strongly depends on the type of analysis and purpose of the underlying research. This way of presenting the resulting data is too static and time consuming. There is a need for a more interactive way of presenting the results. This way a researcher can easily change the parameters, variables and number of points in order to view a plot, or table exactly the way he wants. The produced report should also be easy reproducible. Automating the process of reporting would also make it more reproducible and with less effort.
There are several tools and R packages to make reactive and reproducible reports. But these tools aren’t made to create a full report. Most of the time they are specifically made for the creation of a specific part of the complete report.
Therefore, in the light of this research, an application has been developed which uses the web application framework ‘Shiny’ for R. With this application it should be possible to automate the process of making an omics related report. When the analysis is done, the results can be put in standard objects in R. These objects are used in the shiny-application. This way, a report is made with the values of these objects. By this way, the report is automatically generated. This report is also interactive and gives the information in an orderly manner.
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