Table 2 Databases or tools relate to circRNA profiles, identification, and annotation

GEO

Helping users query and download experiments and curated gene expression profiles

https://www.ncbi.nlm.nih.gov/geo/

[87]

circRNADisease v2.0

Involving in 2964 circRNAs, 416 diseases and 9 species. Facilitating users to browse, search, and download circRNA-disease association data

http://cgga.org.cn:9091/circRNADisease/

[88]

deepBase v3.0

Displaying and analyzing of expression, evolution, function of various ncRNAs, including circRNAs

https://rna.sysu.edu.cn/deepbase3/

[89]

CircAtals 3.0

Integrating the most comprehensive circRNAs and their expression and functional profiles in vertebrates

https://ngdc.cncb.ac.cn/circatlas/

[90]

CircSC

Employing a compendium of full-length single-cell RNA-sequencing datasets and identifying 196,491 human and 310,969 mouse circRNAs

https://ngdc.cncb.ac.cn/circatlas/circSC/index.html

–

CSCD 2.0

Identifying significant number of circRNAs in human cancer and normal tissues/cell lines (~ 2.9 millions)

http://geneyun.net/CSCD2/

[91]

CircNet 2.0

Providing tissue-specific circRNA expression

https://awi.cuhk.edu.cn/~CircNet

[92]

exoRBase v2.0

Providing the comprehensive annotation and expression landscapes of extracellular vesicles long RNAs, which contain mRNA, lncRNA, and circRNA

http://www.exoRBase.org

[93]

MiOncoCirc

Provideing a compendium of circRNAs compiled from cancer clinical samples at The University of Michigan

https://mioncocirc.github.io/

[94]

Circ2Disease

Facilitating users to browse, search, and download circRNA-disease association data

http://bioinformatics.zju.edu.cn/Circ2Disease/index.html

[95]

TSCD

Providing a global view of tissue-specific circRNA in main tissues of human and mouse

http://gb.whu.edu.cn/TSCD

[96]

CircRic

Providing circRNAs expression profile in 935 cancer cell lines from CCLE

https://hanlab.uth.edu/cRic

[97]

CIRI

A tool for identifying de novo circRNAs in RNA-seq data

https://sourceforge.net/projects/ciri/

[28]

CIRCexplorer2

A tool for circRNAs identification and characterization from non-polyadenylated RNA-seq datasets

http://circexplorer2.readthedocs.org

[98]

circRNA_finder

A tool for identifying circRNAs in RNA-seq data

https://github.com/orzechoj/circRNA_finder

[99]

find_circ

A tool for identifying circRNAs in RNA-seq data

https://github.com/marvin-jens/find_circ

[100]

DCC

Applying several logical filters and integrating data across replicate sets to arrive at a precise list of circRNA candidates from sequencing data

https://github.com/dieterich-lab/DCC

[101]

NCLscan

Identifying non-co-linear transcripts with a good balance between sensitivity and precision from RNA-seq data

https://github.com/TreesLab/NCLscan

[102]

circBase

Facilitating users to browse and download gene annotations, and obtain expression details of a particular circRNA

http://www.circbase.org

[103]

CircBank

Including more than 140,000 human annotated circRNA from different source. Allowing users to query the circRNA information based on different search criteria

http://www.circbank.cn

[104]

circVAR

Providing resources for circRNA-related genetic variants in healthy and diseased populations

http://soft.bioinfo-minzhao.org/circvar

[105]

circRNADb

Containing 32,914 annotated exonic circRNAs

http://reprod.njmu.edu.cn/cgi-bin/circrnadb/

[106]