Introduction | Quantification of Exon and Intron features | From BAM or SAM files | From read counts | From transcripts abundances | Analysis of RNA dynamics in time-course experiments | Analysis of Total and Nascent RNA (INSPEcT+) | First guess estimation of the rates | Modeling with sigmoid and impulse functions | Confidence intervals estimation and selection of the regulatory scenario | Quality of the model fit | Selection of the regulative scenario without assumptions on the functional form | Analysis of Total RNA without Nascent (INSPEcT-) | Modeling of the rates with constant, sigmoid and impulse functions | Confidence intervals estimation and model quality | Performance evaluation with simulated data | Generate simulated data with sigmoid and impulsive rates | Generate simulated data with oscillatory rates | Non default parameters for modeling and model selection | Analysis of RNA dynamics in steady state RNA-seq data | Analysis of Total and Nascent RNA | Analysis of Total without Nascent RNA | Wrap-up functions: running INSPEcT with a single command line | Pipeline from BAM files | Pipeline from PCR quantifications | About this document | References

Introduction | Run the application from an R session | Presentation of the Graphical User Interface | Interaction with an object of class INSPEcT | Visualization of the RNA dynamics for a single gene | Model minimization | Interaction with individual parameters of RNA kinetic rates | Assessing rate variability via confidence intervals estimation | De novo hypothesis generation - Case studies | Constant RNA kinetic rates | Modulation of processing rate | Modulation of the synthesis rate | Concomitant modulation of synthesis and degradation rates | Video tutorial | About this document