1 About

Ribo-Seq, short for Ribosome profiling sequencing, is a high-throughput sequencing technology used to study the protein composition and translational efficiency of transcripts in cells. This technique utilizes chemical or biological methods to covalently link ribosomes with the mRNA they are translating at the moment of translation, allowing for only the mRNA bound to ribosomes to be sequenced. This enables the quantitative analysis of the translation levels and positions of each transcript.

There are some tools available for analyzing Ribo-seq sequencing data, which focus on either upstream data processing or downstream data visualization. However, these tools often require users to write shell commands in a Unix system to process raw data and then switch to another IDE to visualize the processed data, which can be quite inconvenient.

For R users, it is more convenient to perform all the necessary tasks within the same environment. Using R functions such as system or system2 allows you to execute shell commands in R, enabling you to call Linux software directly from R. However, it is important to note that many bioinformatics software programs cannot run on Windows.

If you’re using Windows, an alternative option is to use a Windows version of the software built using MinGW tools. Additionally, there are several R-based software programs available to complete the upstream steps, such as Rbowtie2, Rhisat2, and Rsubread.

RiboProfiler integrates the upstream raw data analysis and downstream data visualization. All the steps can be done in R environment. You can also analysis the common ribo-seq and SeRP-seq(Selective ribosome profiling).

Citation: Jun Zhang (2023). RiboProfiler: Integrating Ribo-SEQ Upstream and Downstream Analysis. https://github.com/junjunlab/RiboProfiler

Make sure you have isntalled julia and python. You can install the development version of RiboProfiler:

# install.packages("devtools")
devtools::install_github("junjunlab/RiboProfiler")

# or
remotes::install_github("junjunlab/RiboProfiler")

library(RiboProfiler)

2 Workflow