đź“”   Publications

sangeranalyseR: simple and interactive processing of Sanger sequencing data in R

  Published in Genome Biology and Evolution(GBE), 2021

This package builds on sangerseqR to allow users to create contigs from collections of Sanger sequencing reads. It provides a wide range of options for a number of commonly-performed actions including read trimming, detecting secondary peaks, and detecting indels using a reference sequence. All parameters can be adjusted interactively either in R or in the associated Shiny applications. There is extensive online documentation, and the package can outputs detailed HTML reports, including chromatograms.

  Citation:
K.H. Chao*, K. Barton, S. Palmer, and R. Lanfear* (2021). sangeranalyseR: simple and interactive processing of Sanger sequencing data in R, Genome Biology and Evolution, Volume 13, Issue 3, March 2021, evab028, https://doi.org/10.1093/gbe/evab028.

 

RNASeqR: an R package for automated two-group RNA-Seq analysis workflow

  Published in IEEE/ACM Transactions on Computational Biology and Bioinformatics (TCBB), 2019

This R package is designed for case-control RNA-Seq analysis (two-group). 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.

  Citation:
K.H. Chao, Y.W. Hsiao, Y.F. Lee, C.Y. Lee, L.C. Lai, M.H. Tsai, T.P. Lu, and E.Y. Chuang* (2019). RNASeqR: an R package for automated two-group RNA-Seq analysis workflow, IEEE/ACM Transactions on Computational Biology and Bioinformatics, vol. 18, no. 5, pp. 2023-2031, 1 Sept.-Oct. 2021, doi: 10.1109/TCBB.2019.2956708.