Tag Archives: R package

Most genes in mammals generate several transcript isoforms that differ in stability and translational efficiency through alternative splicing. Such alternative splicing can be tissue- and developmental stage-specific, and such specificity is sometimes associated with disease. Thus, detecting differential isoform usage ...

Next-generation sequencing experiments, such as RNA-Seq, play an increasingly important role in biological research. One complication is that the power and accuracy of such experiments depends substantially on the number of reads sequenced, so it is important and challenging to ...

Identification of genetic variants affecting splicing in RNA sequencing population studies is still in its infancy. Splicing phenotype is more complex than gene expression and ought to be treated as a multivariate phenotype to be recapitulated completely. Here a team ...

The widespread adoption of RNA-seq to quantitatively measure gene expression has increased the scope of sequencing experimental designs to include time course experiments. maSigPro is an R package specifically suited for the analysis of time course gene expression data that ...

compcodeR is an R package for benchmarking of differential expression analysis methods, in particular methods developed for analyzing RNA-seq data. The package provides functionality for simulating realistic RNA-seq count data sets, an interface to several of the most commonly used ...

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 researchers from the University of Copenhagen to develop spliceR, an R package ...