6533b826fe1ef96bd128488e
RESEARCH PRODUCT
Identification and visualization of differential isoform expression in RNA-seq time series
Ana ConesaSonia TarazonaMaría José NuedaJordi Martorell-marugánCristina Martísubject
0301 basic medicineStatistics and ProbabilityGene isoformIdentificationComputer scienceSequence analysisGene ExpressionRNA-SeqComputational biologyBiochemistryBioconductorTranscriptomeMice03 medical and health sciences0302 clinical medicineEstadística e Investigación OperativaRNA IsoformsAnimalsMolecular BiologyGeneVisualizationRegulation of gene expressionB-LymphocytesSequence Analysis RNAGene Expression ProfilingCell DifferentiationApplications NotesComputer Science ApplicationsVisualizationComputational Mathematics030104 developmental biologyGene Expression RegulationComputational Theory and MathematicsRNA-seq time seriesSoftware030217 neurology & neurosurgeryIsoform expressiondescription
Abstract 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. Supplementary information Supplementary data are available at Bioinformatics online.
| year | journal | country | edition | language |
|---|---|---|---|---|
| 2018-01-01 |