BridgeR2

Overview

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).

Installation

# install CRAN released package
install.packages("bridger2")

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

Quick start

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)

Display RNA decay curve

# compare RNA half-lives between two conditions
pvalue_table <- BridgeRPvalueEvaluation(halflife_table,
                                        calibration = TRUE,
                                        save = FALSE)

# show RNA decay curve on RStudio/web browser.
shiny_test <- BridgeReport(pvalue_table)
shiny_test