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Table 1 List of current circRNA analysis workflows

From: nf-core/circrna: a portable workflow for the quantification, miRNA target prediction and differential expression analysis of circular RNAs

Pipeline

Published

Dependencies

CQ

MP

DE

Installation

CirComPara [19]

2017

Python, R or Docker

\(\checkmark\)

\(\times\)

linear RNA

Source code, DockerHub

CirComPara2 [20]

2021

Python, R or Docker

\(\checkmark\)

\(\times\)

\(\times\)

Source code, DockerHub

DEBKS [21]

2021

Python

\(\times\)

\(\times\)

\(\checkmark\)

Source code, Conda, pip

FcircSec [22]

2020

R

\(\times\)

\(\times\)

\(\times\)

CRAN

circRNAProfiler [23]

2020

R

\(\times\)

\(\checkmark\)

\(\checkmark\)

Bioconductor

circtools [24]

2019

Python, R

\(\checkmark\)

\(\times\)

\(\checkmark\)

Conda, Pypi

circMeta [25]

2020

R

\(\times\)

\(\times\)

\(\checkmark\)

Source code via devtools

circRNAwrap [26]

2019

Perl, Python, R

\(\checkmark\)

\(\times\)

\(\checkmark\)

Manual Installation

Ularcirc [27]

2019

R, R Shiny

\(\times\)

\(\checkmark\)

\(\times\)

Bioconductor

nf-core/circrna

2023

Nextflow, java,Docker/Apptainer

\(\checkmark\)

\(\checkmark\)

\(\checkmark\)

DockerHub

  1. CQ circRNA quantification, MP miRNA prediction, DE differential expression