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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.
Health stats visible at Monitor.