In BIMSBbioinfo/ciRcus: Annotation, analysis and visualization of circRNA data

Introduction

ciRcus is a package for easy summarization and exploration of circ RNAs detected in multiple experiments.

Installation

Circ RNA detection

Summarize detected Circ RNAs

library(ciRcus)

The main summarization function in \code{ciRcus} is the \code{summarizeCircs} function. The function takes as input a data.frame which contains minimally 2 columns: 1. sample - sample designation for each file 2. filename - a path to the detected Circ RNAs.

Alternatively, the user can specify supply to the function just the paths to the files, and the coldata will be constructed automatically.

circ.files = list.files(system.file('extdata', package='ciRcus'),
                          pattern='sites.bed',
                          full.names=TRUE)
circ.files = circ.files[!grepl('Sy5y', circ.files)]


coldata = data.frame(sample = sub('.bed','',basename(circ.files)), 
                     file=circ.files)

circs = summarizeCircs(coldata)

circs

Annotate Circs

circs = AnnotatateCircs(circs)

circs

Explore results

Sample statistics

Circ statistics

histogram(circs)

histogram(circs)

Access to CircBase

BIMSBbioinfo/ciRcus documentation built on May 5, 2019, 10:25 a.m.