yuabrahamliu/proRate: proRate is an R package to infer gene transcription rates with a novel least sum of squares method.

The dynamics of transcriptional elongation can influence various biological activities, such as RNA splicing, polyadenylation, and nuclear export. To quantify the elongation rate, a traditional method is to treat cells with drugs that inhibit RNA polymerase II (Pol II) from entering the gene body and then track Pol II with Pro-seq or Gro-seq. However, the data analysis is challenged by the problem of identifying the transition point between the gene regions inhibited by the drug and not, which is necessary to infer the transcription rate. Although the traditional hidden Markov model (HMM) can be used to solve it, this method is complicated with its hidden variable and many parameters to be estimated. Hence, we developed the R package proRate, which identifies the transition point with a novel least sum of squares (LSS) method and then calculates the elongation rate accordingly. The performance on several datasets shows that LSS achieves higher accuracy than HMM. In addition, proRate also covers other functions frequently used in transcription dynamic study, such as metagene plotting, pause index calculation, and gene structure analysis.

install.packages("remotes")
remotes::install_github("yuabrahamliu/proRate")