Identification and visualization of differential isoform expression in RNA-seq time series
Por:
M. NUEDA, J. MARTORELL-MARUGAN, C. MARTI, S. TARAZONA and A. CONESA
Publicada:
1 feb 2018
Resumen:
Motivation: 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.
Results: 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.
Availability and implementation: The package is freely available under the LGPL license from the Bioconductor web site.
Contact: mj.nueda@ua.es or aconesa@ufl.edu
Supplementary information: Supplementary data are available at Bioinformatics online.
Filiaciones:
M. NUEDA:
Univ Alicante, Math Dept, Alicante 03690, Spain
:
Ctr Invest Principe Felipe, Genom Gene Express Lab, Valencia 42012, Spain
:
Ctr Invest Principe Felipe, Genom Gene Express Lab, Valencia 42012, Spain
:
Ctr Invest Principe Felipe, Genom Gene Express Lab, Valencia 42012, Spain
Univ Politecn Valencia, Appl Stat Operat Res & Qual Dept, Valencia 46020, Spain
:
Ctr Invest Principe Felipe, Genom Gene Express Lab, Valencia 42012, Spain
Univ Florida, Microbiol & Cell Sci Dept, Inst Food & Agr Res, Gainesville, FL 32611 USA
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