  Motivation: Alternative splicing is an important mechanism in which the
regions of pre-mRNAs are differentially joined in order to form different
transcript isoforms. Alternative splicing is involved in the regulation of
normal physiological functions but also linked to the development of diseases
such as cancer. We analyse differential expression and splicing using RNA-seq
time series in three different settings: overall gene expression levels,
absolute transcript expression levels and relative transcript expression
levels.
  Results: Using estrogen receptor $\alpha$ signalling response as a model
system, our Gaussian process (GP)-based test identifies genes with differential
splicing and/or differentially expressed transcripts. We discover genes with
consistent changes in alternative splicing independent of changes in absolute
expression and genes where some transcripts change while others stay constant
in absolute level. The results suggest classes of genes with different modes of
alternative splicing regulation during the experiment.
  Availability: R and Matlab codes implementing the method are available at
https://github.com/PROBIC/diffsplicing . An interactive browser for viewing all
model fits is available at http://users.ics.aalto.fi/hande/splicingGP/ .
