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 |