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Bioinformatics Engineering Program Uppsala University School of Engineering

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Bioinformatics Engineering Program

Uppsala University School of Engineering UPTEC X 12 013 Date of issue 2012-06

Author

Jesper Gådin

Title (English)

basicASE: an R-statistics package to detect significant allelic imbalance in RNA-seq data

Title (Swedish)

Abstract

Investigation of allelic imbalance expression QTLs (aeQTLs) in RNA-seq data can increase the accuracy in the hunt for candidate genes susceptible as drug targets. The Bioconductor project has recently developed research tools to handle the massive amounts of data that come with next generation sequencing. The basicASE package has been developed to carry out aeQTL analyses in that environment. Many technical issues concerning a user friendly import, statistical testing and visualization of data are facilitated through the package, which also has a central design to accommodate integration of new functions and development.

Keywords

BasicASE, allelic imbalance, aeQTL, R, Bioconductor, NGS, RNA-seq

Supervisor

Lasse Folkersen

The Center for Molecular Medicine at Karolinska Institute Scientific reviewer

Mikael Thollesson

Department of Organismal Biology at Uppsala University

Project name Sponsors

Language

English Security Secret until 2013-10

ISSN 1401-2138 Classification

Supplementary bibliographical information

Pages

49

Biology Education Centre Biomedical Center Husargatan 3 Uppsala

Box 592 S-75124 Uppsala Tel +46 (0)18 4710000 Fax +46 (0)18 471 4687

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