Identification and visualization of differential isoform expression in RNA-seq time series

Bioinformatics
María José NuedaAna Conesa

Abstract

As sequencing technologies improve their capacity to detect distinct transcripts of the same gene and to address complex experimental designs such as longitudinal studies, there is a need to develop statistical methods for the analysis of isoform expression changes in time series data. Iso-maSigPro is a new functionality of the R package maSigPro for transcriptomics time series data analysis. Iso-maSigPro identifies genes with a differential isoform usage across time. The package also includes new clustering and visualization functions that allow grouping of genes with similar expression patterns at the isoform level, as well as those genes with a shift in major expressed isoform. The package is freely available under the LGPL license from the Bioconductor web site. mj.nueda@ua.es or aconesa@ufl.edu. Supplementary data are available at Bioinformatics online.

Citations

Nov 20, 2012·Nature Methods·Adam Roberts, Lior Pachter
Jun 5, 2014·Bioinformatics·María José NuedaAna Conesa
Jun 19, 2016·Bioinformatics·Yuanhua Huang, Guido Sanguinetti
Mar 30, 2017·BMC Genomics·Sahar AlShareefMagdy M Mahfouz

Related Concepts

Patterns
Genes
Longitudinal Studies
Nucleic Acid Sequencing
Bio-Informatics
Site
Sequencing
License
Protein Isoforms
Analysis

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