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,
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)