Motivation: The dynamic transcriptional mechanisms that govern eukaryotic cell function can now be analyzed by RNA sequencing. However, the packages currently available for the analysis of raw sequencing data do not provide automatic analysis of complex experimental designs with multiple biological conditions and multiple analysis time-points. Results: The MultiRNAflow suite combines several packages in a unified framework allowing exploratory and supervised statistical analyses of temporal data for multiple biological conditions. Availability and implementation: The R package MultiRNAflow is freely available on Bioconductor (https://bioconductor.org/packages/ MultiRNAflow/), and the latest version of the source code is available on a GitHub repository (https://github.com/loubator/MultiRNAflow).