VERSION 1.0.1

Major improvements:

- INSPEcT is now independent from pyhton and HTSeq for counting reads in intronic and exonic regions and now uses the GenomicAlignments and Rsamtools Bioconductor packages functionalities. Thanks to this modification INSPEcT is now fully contained into the R/Bioconductor framework, being therefore more complant with Bioconductor guidelines. Additionally BAM files can be directly used, without the time consuming and memory consuming step of BAM->SAM conversion. Methods related to the creation of the annotation of intronic and exonic features in GTF format to provide to pyhton are now dismissed consequently and will be probably introduced as methods in the Bioconductor package 'compEpiTools'

- Parallel computation is now managed completely within the BiocParallel framework. "newINSPEcT" function and "modelRates" method take as input the argument BPPARAM which is used to handle the parallelization. By default, BPPARAM is assigned with bpparam() function of BiocParallel package, which guarantee the maximum number of available cores used and the usage of forking in Linux and MacOS-X and the usage of the package Snow for Windows machines (nCores methods and arguments are now deprecated)

- Added capabilities for the comparison of two steady-state conditions

- Better estimation of rates in case degDuringPulse=TRUE (newINSPEcT function). Added controls on input arguments in newINSPEcT function. Fixed a bug in the saturation of values out of breaks in inHeatmap method (this change could cause a different clustering order of genes in the heatmap). Added the palette argument to inHeatmap method.

Bug fixes:

- Solved the timeout issue during build/check in Bioc windows server: Removed parallel evaluation from the vignette, removed parallelization during examples execution by the addition of the argument BPPARAM=SerialParam() to modelRates method and newINSPEcT function; reduced the computation time associated to the makeSimModel example code by putting to donotrun the last three lines of code

- Solved two problems. One that occurred during modeling for genes with estimated variance within replicates equal to zero: in these cases the variance is estimated within the time course. A second problem was encountered in the parameter initialization of impulse model: h1 cannot be zero in order to evaluate a finite value."
