SpliceR: an R package for classification of alternative splicing and prediction of coding potential from RNA-seq data.

ABSTRACT:

Background

RNA-seq data is currently underutilized, in part because it is difficult to predict the functional impact of alternate transcription events. Recent software improvements in full-length transcript deconvolution prompted us to develop spliceR, an R package for classification of alternative splicing and prediction of coding potential.

Results

spliceR uses the full-length transcript output from RNA-seq assemblers to detect single or multiple exon skipping, alternative donor and acceptor sites, intron retention, alternative first or last exon usage, and mutually exclusive exon events. For each of these events spliceR also annotates the genomic coordinates of the differentially spliced elements, facilitating downstream sequence analysis. For each transcript isoform frac

SUBMITTER: Vitting-Seerup K 

PROVIDER: S-EPMC3998036 | biostudies-literature | 2014 Mar

REPOSITORIES: biostudies-literature