README.md

In KasperThystrup/circulaR: Characterization of circRNAs from Total RNA-seq data

circulaR

The goal of circulaR is to identify and annotate circular RNA (circRNA) contents from total RNA sequencing data. The package contains functionality for importing chimeric read data generated with the STAR aligner [link: Alexander Dobin - STAR github], filtering backsplice junctions, and overlapping known gene models with the identified backsplice junctions.

Installation

Dependencies

In order to install the circulaR R package, you must ensure to install the following Biocodncutor packages:

• AnnotationDbi
• BiocGenerics
• BSgenome
• DESeq2
• ensembldb
• GenomeInfoDb
• GenomicFeatures
• GenomicRanges
• Gviz
• IRanges
• Rsamtools
• S4Vectors

install.packages("BiocManager")
BiocManager::install(c("AnnotationDbi", "BiocGenerics", "BSgenome", "DESeq2", "ensembldb", "GenomeInfoDb", "GenomicFeatures", "GenomicRanges", "Gviz", "IRanges", "Rsamtools", "S4Vectors"))

In addition, devtools r package must be installed, to enable easy installation of circulaR from github.

install.packages("devtools")
devtools::install_github("https://github.com/KasperThystrup/circulaR")

This should install all dependencies from the official CRAN repository. However, if something does not work out, try to install the CRAN dependencies manually before running the install_github command again:

• dplyr
• ggplot2
• parallel
• pbmcapply
• plyr
• readr
• RSQLite
• stringi
• tibble
• tidyr
• Hmisc

install.packages(c("dplyr", "ggplot2", "parallel", "pbmcapply", "plyr", "readr", "RSQLite", "stringi", "tibble", "tidyr", "Hmisc"))
devtools::install_github("https://github.com/KasperThystrup/circulaR")

KasperThystrup/circulaR documentation built on March 14, 2021, 12:44 p.m.