Changes in version 1.1.1                        

Changes were made to ensure that R CMD check runs without errors or
warnings. Moreover, MIRit has been updated to use the new miRTarBase
version 10 database.

                       Changes in version 0.99.13                       

A minor fix was made to fix the undefined variables note during R CMD
check.

                       Changes in version 0.99.12                       

This version includes several improvements, including a completely
revised vignette where all chunks are evaluated, minor tweaks to default
values for differential expression analysis, and some bug fixes to the
error bars in the plotDE() function. Other issues, such as artifacts in
show methods, lacks in documentation, and dependence in DESCRIPTION,
have been addressed too.

                       Changes in version 0.99.11                       

This new version introduces the possibility of limiting validated
targets retrieval from miRTarBase to only those interactions supported
by extensive experimental evidence. Moreover, minor fixes were made to
the vignette, documentation, and internal data. Finally, some examples
have been redefined to reduce checking time.

                       Changes in version 0.99.10                       

This patch introduces a minor fix for one unit test.

                       Changes in version 0.99.9                        

With this version, significant p-values originating from functional
enrichment analyses now include extreme values. Further, examples have
been shortened and unit tests now use smaller datasets.

                       Changes in version 0.99.8                        

This patch further reduces R CMD check time by limiting unnecessary
examples and by using smaller datasets for unit tests.

                       Changes in version 0.99.7                        

This version introduces parallel computing capabilities for the
mirnaIntegration() function. This is particularly useful for Boschloo's
exact test, whose execution is now faster. Moreover, the test suite has
been redefined to reduce running times.

                       Changes in version 0.99.6                        

The testing suite has been redefined to allow different results for
different versions of packages employed in differential expression
analysis.

                       Changes in version 0.99.5                        

This update fixes a bug in the batchCorrection() function that prevented
the correct use of this function with newer versions of the
MultiAssayExperiment package.

                       Changes in version 0.99.4                        

After the implementation of the IS_BIOC_BUILD_MACHINE variable to the
Single Package Builder (SPB), this version bump drives a new build to
fix errors during R CMD check on SPB.

                       Changes in version 0.99.3                        

This version fixes a bug in the topologicalAnalysis() function that
prevented the use of a functional progress bar during permutation
testing. Moreover, the example for the addDifferentialExpression()
function has been updated to reduce its running time.

                       Changes in version 0.99.2                        

MIRit now allows to filter the pathways used for topological analysis
based on the number of nodes.

                       Changes in version 0.99.1                        

Functional enrichment analyses and TAIPA now use cached databases to
reduce running times.

                       Changes in version 0.99.0                        

Initial version for Bioconductor submission.