README.md

In elmerfer/ArribaR: gene Expression quantification, Gene Fusion detection and Immuno Content Deconvolution by STAR and ARRIBA softwares

ArribaR

ArribaR is an R based platform for Gene Expression and Gene Fusion identification based on the STAR aligner and the Arriba fusion detector. It is part of an analytical suite for the study of genomic rearrangements, its potential as target therapy and as neoantigenic role. In addition it may provide the immune microenvironment by MIXTURE by the LM22 molecular signature The ArribaR software package is intended to provide a friendly and effortless R tool for non bioinformatics. It isolates all the requirements to run both softwares in an easy and transparent fashion, simplifying the installation process and execution. It automatically download and install the basic softwares (STAR + Arriba) extra files, like the genome references and annotations should be downloaded using the GenomeDB and Aligners R packages of this family Next Generation Sequencing platform.

Getting Started

Please visit GenomeDB and Aligners.

*Install the Human Genome

*Install and build the STAR reference index

Install ArribaR package

install.packages("devtools")
library(devtools)
install_github("elmerfer/ArribaR")

Install Arriba software dependencies

InstallArribaR()

<<<<<<< HEAD The instalation will be performed under the GenomeDB organization ======= This may take a long time and it will do the following process minimal installation of the STAR version 2.7.6a (the one required for Arriba version 2.1.0) the GRCc37(Hg19) Human reference file the GENCODE GTF annotation file build the human reference index file * minimal installation of the Arriba software 2.1.0

as a result it will leave an organized "Software" folder at where/I/want/to/install/path/Software

Usage

This implementation is specifically provided to process human RNAseq paired data, thus requiring to hold both xxxx_1.fastq(.gz) and xxxx_2.fastq(.gz). The row sequencing data should be "xxxxx_1.fastq" or "xxxxx_1.fastq.gz". The second sequence file will be automatically defined as "xxxxx_2.fastq" or "xxxxx_2.fastq.gz"

library(ArribaR)
test.subject <- GetArribaRTest()
bam.subject <- RunSTARforARRIBA(test.subject)
Fusions <- RunARRIBA(bam.subject)
View(Fusions)

Interactive usage

copy this R script in your RStudio and source it library(stringr) select <- file.choose() if(length(select)>0){ bam.file <-RunSTARforARRIBA(sbjFile = select, nThreads = 10L) RunARRIBA(bam.file) sorted.bam.file <- RunSortIndexBam(bam.file, remove = F) FusionPlot(sorted.bam.file, savePlot = T) }else{ cat("No File selected") }

Authors

• Elmer A. Fernández CIDIE-UCC-CONICET

elmerfer/ArribaR documentation built on Nov. 14, 2023, 1 p.m.