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Leiden University of Applied Sciences

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Traineeship proposition

Abstract 2018-2019: Development of an interactive application for transcriptome analysis 

The Leiden Centre of Applied Bioscience’s bioinformatics lab is responsible for the bioinformatics support of different lectorates. Currently, each gene expression analysis project is analyzed in with custom methods. An RNA-seq analysis is performed for each dataset, and the best method for doing this is evaluated. This however results in variation between the processed datasets, which makes comparing these needlessly difficult. Because of the large amounts of data the LCAB has to process, the creation of a standard application for the RNA-seq analysis that gives a standardized output is necessary. Additionally, this application has to be compatible with the existing application AVIDE, which visualizes RNA-seq data in a statistical manner. Through the use of R-shiny and with AVIDE as a reference, AIDEA was created. Its user interface was directly inspired by that of AVIDE, and it expands on the data processing functions already present in said application. AIDEA requires a “sample sheet” and a “fragments per gene” file to be uploaded, which it uses to calculate various variables by using the DESeq2 and edgeR package. The user can choose which package to use. Output is generated in the form of several data tables, which can be downloaded in either .tsv or .csv format. Genes of interest can be selected, stored in a separate table, and downloaded as well. 


Zernikestraat 10
2300 AJ Leiden


Traineeship supervisor
Floyd F.Wittink
Traineeship supervisor
Stephen S. Pieterman
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