RNASeqR: RNA-Sequencing pipeline R package development

   April 01, 2018 - December 31, 2018

   Taipei, Taiwan

   Bioinformatics and Biostatistics Core Lab, Center of Genomic and Precision Medicine, National Taiwan University

   Undergraduate research student

   Published   IEEE/ACM Transactions on Computational Biology and Bioinformatics

     Eric Y. Chuang       Tzu-pin Lu  


I developed RNASeqR for two-group (case-control) RNA-Seq analysis and it is now available on Bioconductor 3.10 release. There are six steps: “RNASeqRParam S4 Object Creation”, “Environment Setup”, “Quality Assessment”, “Reads Alignment & Quantification”, “Gene-level Differential Analyses” and “Functional Analyses”. Each step corresponds to a function in this package. After running functions in order, a basic RNASeq analysis would be done easily.

In December, 2018, I presented this work in NTU Centers of Genomics and Precision Medicine (NTUCGM) Summer Research competition and won the first prize among all summer research students. In June, 2019, I oral presented this work in ICIBM 2019, Columbus, USA. The manuscript is now published in IEEE/ACM Transactions on Computational Biology and Bioinformatics.

Selected visual results of gene-level differential analyses from RNASeqR.

  Source code & Documentation