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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)These binaries (installable software) and packages are in development.
They may not be fully stable and should be used with caution. We make no claims about them.