Genome-Wide RNA Degradation Analysis Using BRIC-Seq Data

BRIC-seq is a genome-wide approach for determining RNA stability in mammalian cells. This package provides a series of functions for performing quality check of your BRIC-seq data, calculation of RNA half-life for each transcript and comparison of RNA half-lives between two conditions.


BRIC-seq is a genome-wide approach for determining RNA stalibity in mammalian cells. bridger2 provides a series of functions for performing a comprehensive BRIC-seq data analysis. After estimating the RPKM values for all genes from your BRIC-seq fastq files, you can easily analyze your BRIC-seq data using bridger2 R package.

To make that happen, bridger2:

  • Checks the quality of your BRIC-seq data.

  • Normalizes RPKM values of your BRIC-seq data.

  • Calculates RNA half-life for each transcript

  • Compares RNA half-lives between two conditions.

  • Displays RNA decay curve using a web browser (powered by shiny).

# The the development version from GitHub:
# install.packages("devtools")
devtools::install_github("Imamachi-n/BridgeR2")

Here I show the most basic step for analyzing your BRIC-seq data. This step require matrix object (named RNA_halflife_comparison in this case) of the RPKM values from your BRIC-seq data. BridgeRCore function returns data.table object including RNA half-life, R2 and the selected fitting model.

halflife_table <- BridgeRCore(RNA_halflife_comparison)

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install.packages("bridger2")

0.1.0 by Naoto Imamachi, 10 months ago


Browse source code at https://github.com/cran/bridger2


Authors: Naoto Imamachi [aut, cre]


Documentation:   PDF Manual  


MIT + file LICENSE license


Imports data.table, ggplot2, shiny, shinydashboard, plotly, BSDA, outliers

Suggests testthat


See at CRAN