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INSPEcT / INference of Synthesis Processing and dEgradation rates in Time-course analysis

Allows to analyze 4sU- and RNA-seq data. INSPEcT can determine the probability of a given combination of rate to regulate the gene expression during the time-course by modeling and comparing alternative scenarios of transcriptional regulation. This tools allows to test the performance given a dataset and predict how many additional replicates and time points would be needed to reach the desired performance.

HALO / Half-life Organizer

Allows the precise determination of transcript half-lives from measurements of RNA de novo transcription or decay determined with microarrays or RNA-seq. HALO is an extensible Java framework providing state-of-the-art methods for transcript half-life calculation as well as quality control, filtering and normalization. It can be integrated into other gene expression profiling frameworks or can be used as a standalone. It aims to calculate transcript half-lives in a fast and straightforward way from new measurements of de novo synthesis and/or decay both for microarrays or RNA-seq.